0.017813
0.000000
0.000000
0.000000
0.006120
0.000000
0.000000
0.000000
0.025208
0.00000
0.00000
0.00000
Gao, X.P.
Waltersperger, S.
Wang, M.T.
Cui, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
56.140
163.400
39.670
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
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA 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
O
N
75
N
P
N
76
N
O
N
77
N
O
N
78
N
O
N
79
N
C
N
80
R
C
N
81
N
O
N
82
S
C
N
83
N
O
N
84
N
C
N
85
R
C
Y
86
N
N
Y
87
N
C
Y
88
N
N
Y
89
N
C
Y
90
N
C
N
91
N
N
Y
92
N
N
Y
93
N
C
Y
94
N
N
Y
95
N
C
N
96
N
H
N
97
N
H
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
H
N
109
N
H
N
110
N
O
N
111
N
P
N
112
N
O
N
113
N
O
N
114
N
O
N
115
N
C
N
116
R
C
N
117
N
O
N
118
S
C
N
119
N
O
N
120
N
C
N
121
R
C
N
122
N
N
N
123
N
C
N
124
N
O
N
125
N
N
N
126
N
C
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
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
P
N
146
N
O
N
147
N
O
N
148
N
O
N
149
N
C
N
150
R
C
N
151
N
O
N
152
S
C
N
153
N
O
N
154
N
C
N
155
R
C
Y
156
N
N
Y
157
N
C
Y
158
N
N
Y
159
N
C
N
160
N
C
N
161
N
O
N
162
N
N
N
163
N
C
N
164
N
N
N
165
N
N
Y
166
N
C
N
167
N
H
N
168
N
H
N
169
N
H
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
O
N
182
N
P
N
183
N
O
N
184
N
O
N
185
N
O
N
186
N
C
N
187
R
C
N
188
N
O
N
189
S
C
N
190
N
O
N
191
N
C
N
192
R
C
N
193
N
N
N
194
N
C
N
195
N
O
N
196
N
N
N
197
N
C
N
198
N
O
N
199
N
C
N
200
N
C
N
201
N
C
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
H
N
217
N
N
N
218
S
C
N
219
N
C
N
220
N
O
N
221
N
C
N
222
N
C
N
223
N
C
N
224
N
O
N
225
N
N
N
226
N
O
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
H
N
237
N
N
N
238
S
C
N
239
N
C
N
240
N
O
N
241
N
C
N
242
N
C
N
243
N
C
N
244
N
O
N
245
N
O
N
246
N
O
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
N
C
N
258
N
C
N
259
N
O
N
260
N
O
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
N
N
267
S
C
N
268
N
C
N
269
N
O
N
270
N
C
Y
271
N
C
Y
272
N
N
Y
273
N
C
Y
274
N
C
Y
275
N
N
N
276
N
O
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
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
O
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
S
C
N
295
N
C
N
296
N
C
N
297
N
C
N
298
N
O
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
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
N
N
313
S
C
N
314
N
C
N
315
N
O
N
316
N
C
N
317
N
C
N
318
N
C
N
319
N
C
N
320
N
O
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
H
N
332
N
H
N
333
N
H
N
334
N
N
N
335
S
C
N
336
N
C
N
337
N
O
N
338
N
C
N
339
N
C
N
340
N
C
N
341
N
C
N
342
N
N
N
343
N
O
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
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
N
N
360
S
C
N
361
N
C
N
362
N
O
N
363
N
C
N
364
N
C
N
365
N
S
N
366
N
C
N
367
N
O
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
H
N
379
N
N
N
380
S
C
N
381
N
C
N
382
N
O
N
383
N
C
Y
384
N
C
Y
385
N
C
Y
386
N
C
Y
387
N
C
Y
388
N
C
Y
389
N
C
N
390
N
O
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
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
N
N
403
S
C
N
404
N
C
N
405
N
O
N
406
N
C
N
407
N
C
N
408
N
C
N
409
N
O
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
N
N
420
S
C
N
421
N
C
N
422
N
O
N
423
N
C
N
424
N
O
N
425
N
O
N
426
N
H
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
N
N
434
S
C
N
435
N
C
N
436
N
O
N
437
R
C
N
438
N
O
N
439
N
C
N
440
N
O
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
H
N
450
N
N
N
451
S
C
N
452
N
C
N
453
N
O
N
454
N
C
Y
455
N
C
Y
456
N
C
Y
457
N
C
Y
458
N
C
Y
459
N
C
Y
460
N
C
N
461
N
O
N
462
N
O
N
463
N
H
N
464
N
H
N
465
N
H
N
466
N
H
N
467
N
H
N
468
N
H
N
469
N
H
N
470
N
H
N
471
N
H
N
472
N
H
N
473
N
H
N
474
N
N
N
475
S
C
N
476
N
C
N
477
N
O
N
478
N
C
N
479
N
C
N
480
N
C
N
481
N
O
N
482
N
H
N
483
N
H
N
484
N
H
N
485
N
H
N
486
N
H
N
487
N
H
N
488
N
H
N
489
N
H
N
490
N
H
N
491
N
H
N
492
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
doub
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
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
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
Y
93
N
sing
Y
94
N
sing
Y
95
N
doub
N
96
N
sing
Y
97
N
sing
Y
98
N
sing
Y
99
N
doub
N
100
N
sing
Y
101
N
doub
N
102
N
sing
N
103
N
sing
Y
104
N
sing
Y
105
N
doub
N
106
N
sing
Y
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
doub
N
111
N
sing
N
112
N
sing
N
113
N
sing
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
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
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
doub
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
doub
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
Y
166
N
sing
Y
167
N
sing
Y
168
N
doub
N
169
N
sing
Y
170
N
sing
N
171
N
sing
Y
172
N
doub
N
173
N
doub
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
doub
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
doub
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
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
doub
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
doub
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
doub
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
doub
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
doub
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
doub
N
253
N
sing
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
doub
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
doub
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
Y
276
N
sing
Y
277
N
doub
Y
278
N
doub
N
279
N
sing
Y
280
N
sing
N
281
N
sing
Y
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
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
doub
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
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
sing
N
313
N
sing
N
314
N
sing
N
315
N
doub
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
sing
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
N
335
N
sing
N
336
N
doub
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
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
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
doub
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
sing
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
doub
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
Y
384
N
doub
Y
385
N
sing
Y
386
N
sing
N
387
N
sing
Y
388
N
doub
N
389
N
sing
Y
390
N
doub
N
391
N
sing
Y
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
doub
N
403
N
sing
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
doub
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
doub
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
sing
N
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
doub
N
449
N
sing
N
450
N
sing
N
451
N
sing
N
452
N
sing
Y
453
N
doub
Y
454
N
sing
Y
455
N
sing
N
456
N
sing
Y
457
N
doub
N
458
N
sing
Y
459
N
doub
N
460
N
sing
Y
461
N
sing
N
462
N
sing
N
463
N
sing
N
464
N
sing
N
465
N
sing
N
466
N
sing
N
467
N
sing
N
468
N
sing
N
469
N
sing
N
470
N
sing
N
471
N
sing
N
472
N
doub
N
473
N
sing
N
474
N
sing
N
475
N
sing
N
476
N
sing
N
477
N
sing
N
478
N
sing
N
479
N
sing
N
480
N
sing
N
481
N
sing
N
482
N
sing
N
483
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
41
10529
10541
10.1093/nar/gkt748
23985969
Structural insights into VirB-DNA complexes reveal mechanism of transcriptional activation of virulence genes
2013
10.2210/pdb3w3c/pdb
pdb_00003w3c
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
2012-12-12
ADSC QUANTUM 315r
double crystal
SINGLE WAVELENGTH
M
x-ray
1
1.54001
1.0
BL17U
SSRF
1.54001
SYNCHROTRON
SSRF BEAMLINE BL17U
16254.703
Virulence regulon transcriptional activator VirB
UNP residues 129-250
1
man
polymer
8097.236
DNA (26-MER)
1
syn
polymer
7875.119
DNA (26-MER)
1
syn
polymer
18.015
water
70
nat
water
Cell invasion regulator InvE
no
no
MGSSHHHHHHSSGLVPRGSHMAKEHSIRELGIGLNFLKVSGMSYKDIAKKENLSRAKVTRAFQAASVPQEIISLFPIASE
LNFNDYKILFNYYKGLEKANESLSSTLPILKEEIKDLDTNLPPDIYKKEILNIIKKSKNRKQN
MGSSHHHHHHSSGLVPRGSHMAKEHSIRELGIGLNFLKVSGMSYKDIAKKENLSRAKVTRAFQAASVPQEIISLFPIASE
LNFNDYKILFNYYKGLEKANESLSSTLPILKEEIKDLDTNLPPDIYKKEILNIIKKSKNRKQN
A
polypeptide(L)
no
no
(DT)(DT)(DT)(DG)(DT)(DG)(DG)(DG)(DA)(DT)(DT)(DT)(DC)(DA)(DT)(DG)(DA)(DT)(DG)(DA)
(DA)(DA)(DC)(DG)(DA)(DG)
TTTGTGGGATTTCATGATGAAACGAG
B
polydeoxyribonucleotide
no
no
(DA)(DA)(DA)(DC)(DT)(DC)(DG)(DT)(DT)(DT)(DC)(DA)(DT)(DC)(DA)(DT)(DG)(DA)(DA)(DA)
(DT)(DC)(DC)(DC)(DA)(DC)
AAACTCGTTTCATCATGAAATCCCAC
C
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
301
sample
virB
42897
Shigella flexneri 2a
562
Escherichia coli
Rosetta DE3
Plasmid
pET-28a
1
2.82
56.43
VAPOR DIFFUSION
4.3
0.1M MgCl2, 0.1M Sodium Acetate, 30% PEG400, 8%(v/v)1,3-Butanediol, pH 4.3, VAPOR DIFFUSION, temperature 295K
295
-11.676
1
19
B
4
C
26
8.736
B_DG4:DC26_C
1
-14.897
-0.966
-0.244
-0.151
-1.730
1
20
B
5
C
25
-3.038
B_DT5:DA25_C
2
-16.329
-0.218
0.293
-0.178
-7.477
1
19
B
6
C
24
1.303
B_DG6:DC24_C
3
-7.552
-0.554
-0.283
-0.213
14.193
1
19
B
7
C
23
3.880
B_DG7:DC23_C
4
-6.125
-0.096
0.232
-0.128
9.663
1
19
B
8
C
22
0.497
B_DG8:DC22_C
5
-16.090
0.041
0.345
0.020
-5.704
1
20
B
9
C
21
-0.593
B_DA9:DT21_C
6
-16.929
0.058
0.139
-0.114
-1.446
1
20
B
10
C
20
0.934
B_DT10:DA20_C
7
-19.632
-0.045
0.366
-0.041
-6.315
1
20
B
11
C
19
0.423
B_DT11:DA19_C
8
-20.656
-0.270
0.098
-0.178
-13.114
1
20
B
12
C
18
-0.604
B_DT12:DA18_C
9
-31.173
-0.068
0.166
-0.044
-21.830
1
19
B
13
C
17
0.109
B_DC13:DG17_C
10
-5.894
0.179
0.494
-0.140
-0.914
1
20
B
14
C
16
4.264
B_DA14:DT16_C
11
-13.614
0.087
0.263
0.030
-2.051
1
20
B
15
C
15
5.025
B_DT15:DA15_C
12
-18.726
-0.231
-0.046
-0.027
-3.724
1
19
B
16
C
14
3.397
B_DG16:DC14_C
13
-10.241
-0.204
-0.283
-0.068
1.932
1
20
B
17
C
13
2.614
B_DA17:DT13_C
14
-13.659
0.108
0.177
-0.064
0.997
1
20
B
18
C
12
2.319
B_DT18:DA12_C
15
-10.429
-0.025
0.129
-0.211
2.558
1
19
B
19
C
11
1.818
B_DG19:DC11_C
16
-3.389
-0.577
-0.245
-0.375
-9.714
1
20
B
20
C
10
-0.313
B_DA20:DT10_C
17
-20.375
0.522
-0.358
-0.132
-4.193
1
20
B
21
C
9
-2.668
B_DA21:DT9_C
18
-13.156
-0.469
-0.022
-0.133
-7.372
B
22
C
8
10.857
B_DA22:DT8_C
19
-12.435
1.081
-0.520
0.125
-1.819
1
19
B
23
C
7
-0.004
B_DC23:DG7_C
20
-14.091
0.329
0.361
-0.211
3.492
1
19
B
24
C
6
-5.292
B_DG24:DC6_C
21
-22.800
0.214
0.032
0.038
1.912
1
20
B
25
C
5
4.468
B_DA25:DT5_C
22
-12.724
-0.400
0.179
-0.143
-1.715
1
19
B
26
C
4
-3.552
B_DG26:DC4_C
23
-18.540
0.494
0.805
0.136
3.207
33.788
B
B
4
5
0.662
C
C
26
25
3.109
0.381
-0.795
-0.074
BB_DG4DT5:DA25DC26_CC
1
-7.873
13.664
32.882
-0.187
0.120
3.325
43.899
B
B
5
6
-6.837
C
C
25
24
3.540
-5.097
0.091
1.734
BB_DT5DG6:DC24DA25_CC
2
3.052
-4.094
43.515
2.829
0.183
2.614
26.827
B
B
6
7
19.027
C
C
24
23
2.767
8.645
0.539
0.293
BB_DG6DG7:DC23DC24_CC
3
-3.784
8.327
25.141
-1.267
-1.991
3.457
37.983
B
B
7
8
1.228
C
C
23
22
3.390
0.798
-0.913
0.128
BB_DG7DG8:DC22DC23_CC
4
-3.333
5.128
37.833
0.091
0.957
3.565
42.148
B
B
8
9
-1.404
C
C
22
21
3.557
-1.009
-0.312
-0.345
BB_DG8DA9:DT21DC22_CC
5
-0.104
0.145
42.136
-0.366
0.423
3.263
32.714
B
B
9
10
-12.817
C
C
21
20
3.141
-7.157
-0.211
-0.878
BB_DA9DT10:DA20DT21_CC
6
-2.441
4.370
31.852
-0.331
-0.044
3.231
38.336
B
B
10
11
-5.270
C
C
20
19
3.242
-3.451
0.063
-0.115
BB_DT10DT11:DA19DA20_CC
7
3.798
-5.800
38.004
0.254
0.376
3.324
39.604
B
B
11
12
-0.093
C
C
19
18
3.324
-0.063
-0.345
0.097
BB_DT11DT12:DA18DA19_CC
8
-0.044
0.065
39.604
0.150
0.504
3.537
39.577
B
B
12
13
0.059
C
C
18
17
3.574
0.040
0.729
0.768
BB_DT12DC13:DG17DA18_CC
9
-1.896
2.801
39.533
1.129
-1.318
2.952
31.879
B
B
13
14
22.549
C
C
17
16
2.837
12.088
0.063
0.856
BB_DC13DA14:DT16DG17_CC
10
1.035
-1.930
29.536
-0.469
0.059
3.269
29.258
B
B
14
15
4.397
C
C
16
15
3.349
2.217
-0.043
-0.772
BB_DA14DT15:DA15DT16_CC
11
2.300
-4.562
29.087
-2.016
0.590
3.575
39.648
B
B
15
16
3.525
C
C
15
14
3.483
2.388
0.557
1.220
BB_DT15DG16:DC14DA15_CC
12
2.542
-3.752
39.500
1.497
-0.501
3.172
35.424
B
B
16
17
3.285
C
C
14
13
3.115
1.989
-0.617
0.054
BB_DG16DA17:DT13DC14_CC
13
-6.016
9.937
34.871
-0.195
0.157
3.449
32.638
B
B
17
18
-1.750
C
C
13
12
3.433
-0.983
0.194
-0.613
BB_DA17DT18:DA12DT13_CC
14
-0.023
0.041
32.624
-0.912
-0.350
3.148
27.600
B
B
18
19
16.646
C
C
12
11
3.304
7.834
0.257
-0.118
BB_DT18DG19:DC11DA12_CC
15
1.199
-2.548
26.459
-2.172
-0.245
3.653
41.476
B
B
19
20
0.189
C
C
11
10
3.622
0.134
-0.787
0.258
BB_DG19DA20:DT10DC11_CC
16
-1.897
2.680
41.434
0.348
0.887
2.904
30.599
B
B
20
21
4.516
C
C
10
9
2.946
2.377
-0.098
-0.400
BB_DA20DA21:DT9DT10_CC
17
-2.924
5.554
30.371
-1.180
-0.334
3.475
41.321
B
B
21
22
-7.340
C
C
9
8
3.479
-5.157
0.191
-0.177
BB_DA21DA22:DT8DT9_CC
18
4.727
-6.729
40.750
0.342
0.273
2.394
30.878
B
B
22
23
30.510
C
C
8
7
3.007
15.472
-0.367
-0.487
BB_DA22DC23:DG7DT8_CC
19
-4.629
9.127
26.407
-3.602
-0.115
3.242
37.007
B
B
23
24
9.593
C
C
7
6
3.350
6.057
-0.290
-0.202
BB_DC23DG24:DC6DG7_CC
20
3.097
-4.905
36.398
-1.146
0.880
3.305
30.186
B
B
24
25
1.699
C
C
6
5
3.324
0.884
0.293
-0.007
BB_DG24DA25:DT5DC6_CC
21
-1.444
2.773
30.139
-0.197
-0.861
3.242
37.342
B
B
25
26
1.816
C
C
5
4
3.332
1.156
0.117
-0.365
BB_DA25DG26:DC4DT5_CC
22
-7.098
11.151
36.668
-0.724
-1.133
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
repository
Initial release
Database references
Database references
Data collection
Database references
Refinement description
1
0
2013-09-04
1
1
2013-12-11
1
2
2013-12-25
1
3
2023-11-08
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
PDBJ
Y
PDBJ
2012-12-19
REL
REL
HOH
water
synthetic DNA
sample
synthetic DNA
sample
3VWB
PDB entry: 3VWB
PDB
experimental model
HOH
1
4
HOH
HOH
301
A
HOH
2
4
HOH
HOH
302
A
HOH
4
4
HOH
HOH
303
A
HOH
6
4
HOH
HOH
304
A
HOH
7
4
HOH
HOH
305
A
HOH
8
4
HOH
HOH
306
A
HOH
9
4
HOH
HOH
307
A
HOH
10
4
HOH
HOH
308
A
HOH
12
4
HOH
HOH
309
A
HOH
14
4
HOH
HOH
310
A
HOH
15
4
HOH
HOH
311
A
HOH
16
4
HOH
HOH
312
A
HOH
20
4
HOH
HOH
313
A
HOH
27
4
HOH
HOH
314
A
HOH
30
4
HOH
HOH
315
A
HOH
31
4
HOH
HOH
316
A
HOH
32
4
HOH
HOH
317
A
HOH
38
4
HOH
HOH
318
A
HOH
39
4
HOH
HOH
319
A
HOH
40
4
HOH
HOH
320
A
HOH
41
4
HOH
HOH
321
A
HOH
47
4
HOH
HOH
322
A
HOH
48
4
HOH
HOH
323
A
HOH
49
4
HOH
HOH
324
A
HOH
50
4
HOH
HOH
325
A
HOH
52
4
HOH
HOH
326
A
HOH
53
4
HOH
HOH
327
A
HOH
54
4
HOH
HOH
328
A
HOH
55
4
HOH
HOH
329
A
HOH
56
4
HOH
HOH
330
A
HOH
60
4
HOH
HOH
331
A
HOH
62
4
HOH
HOH
332
A
HOH
63
4
HOH
HOH
333
A
HOH
65
4
HOH
HOH
334
A
HOH
66
4
HOH
HOH
335
A
HOH
70
4
HOH
HOH
336
A
HOH
69
4
HOH
HOH
337
A
HOH
5
4
HOH
HOH
101
B
HOH
11
4
HOH
HOH
102
B
HOH
17
4
HOH
HOH
103
B
HOH
21
4
HOH
HOH
104
B
HOH
23
4
HOH
HOH
105
B
HOH
25
4
HOH
HOH
106
B
HOH
26
4
HOH
HOH
107
B
HOH
29
4
HOH
HOH
108
B
HOH
33
4
HOH
HOH
109
B
HOH
34
4
HOH
HOH
110
B
HOH
37
4
HOH
HOH
111
B
HOH
43
4
HOH
HOH
112
B
HOH
44
4
HOH
HOH
113
B
HOH
46
4
HOH
HOH
114
B
HOH
51
4
HOH
HOH
115
B
HOH
57
4
HOH
HOH
116
B
HOH
58
4
HOH
HOH
117
B
HOH
61
4
HOH
HOH
118
B
HOH
64
4
HOH
HOH
119
B
HOH
3
4
HOH
HOH
101
C
HOH
13
4
HOH
HOH
102
C
HOH
18
4
HOH
HOH
103
C
HOH
19
4
HOH
HOH
104
C
HOH
22
4
HOH
HOH
105
C
HOH
24
4
HOH
HOH
106
C
HOH
28
4
HOH
HOH
107
C
HOH
35
4
HOH
HOH
108
C
HOH
36
4
HOH
HOH
109
C
HOH
42
4
HOH
HOH
110
C
HOH
45
4
HOH
HOH
111
C
HOH
59
4
HOH
HOH
112
C
HOH
67
4
HOH
HOH
113
C
HOH
68
4
HOH
HOH
114
C
n
1
108
A
n
2
109
A
n
3
110
A
n
4
111
A
n
5
112
A
n
6
113
A
n
7
114
A
n
8
115
A
n
9
116
A
n
10
117
A
n
11
118
A
n
12
119
A
n
13
120
A
n
14
121
A
n
15
122
A
n
16
123
A
n
17
124
A
n
18
125
A
n
19
126
A
n
20
127
A
n
21
128
A
n
22
129
A
n
23
130
A
GLU
131
n
24
GLU
131
A
HIS
132
n
25
HIS
132
A
SER
133
n
26
SER
133
A
ILE
134
n
27
ILE
134
A
ARG
135
n
28
ARG
135
A
GLU
136
n
29
GLU
136
A
LEU
137
n
30
LEU
137
A
GLY
138
n
31
GLY
138
A
ILE
139
n
32
ILE
139
A
GLY
140
n
33
GLY
140
A
LEU
141
n
34
LEU
141
A
ASN
142
n
35
ASN
142
A
PHE
143
n
36
PHE
143
A
LEU
144
n
37
LEU
144
A
LYS
145
n
38
LYS
145
A
VAL
146
n
39
VAL
146
A
SER
147
n
40
SER
147
A
GLY
148
n
41
GLY
148
A
MET
149
n
42
MET
149
A
SER
150
n
43
SER
150
A
TYR
151
n
44
TYR
151
A
LYS
152
n
45
LYS
152
A
ASP
153
n
46
ASP
153
A
ILE
154
n
47
ILE
154
A
ALA
155
n
48
ALA
155
A
LYS
156
n
49
LYS
156
A
LYS
157
n
50
LYS
157
A
GLU
158
n
51
GLU
158
A
ASN
159
n
52
ASN
159
A
LEU
160
n
53
LEU
160
A
SER
161
n
54
SER
161
A
ARG
162
n
55
ARG
162
A
ALA
163
n
56
ALA
163
A
LYS
164
n
57
LYS
164
A
VAL
165
n
58
VAL
165
A
THR
166
n
59
THR
166
A
ARG
167
n
60
ARG
167
A
ALA
168
n
61
ALA
168
A
PHE
169
n
62
PHE
169
A
GLN
170
n
63
GLN
170
A
ALA
171
n
64
ALA
171
A
ALA
172
n
65
ALA
172
A
SER
173
n
66
SER
173
A
VAL
174
n
67
VAL
174
A
PRO
175
n
68
PRO
175
A
GLN
176
n
69
GLN
176
A
GLU
177
n
70
GLU
177
A
ILE
178
n
71
ILE
178
A
ILE
179
n
72
ILE
179
A
SER
180
n
73
SER
180
A
LEU
181
n
74
LEU
181
A
PHE
182
n
75
PHE
182
A
PRO
183
n
76
PRO
183
A
ILE
184
n
77
ILE
184
A
ALA
185
n
78
ALA
185
A
SER
186
n
79
SER
186
A
GLU
187
n
80
GLU
187
A
LEU
188
n
81
LEU
188
A
ASN
189
n
82
ASN
189
A
PHE
190
n
83
PHE
190
A
ASN
191
n
84
ASN
191
A
ASP
192
n
85
ASP
192
A
TYR
193
n
86
TYR
193
A
LYS
194
n
87
LYS
194
A
ILE
195
n
88
ILE
195
A
LEU
196
n
89
LEU
196
A
PHE
197
n
90
PHE
197
A
ASN
198
n
91
ASN
198
A
TYR
199
n
92
TYR
199
A
TYR
200
n
93
TYR
200
A
LYS
201
n
94
LYS
201
A
GLY
202
n
95
GLY
202
A
LEU
203
n
96
LEU
203
A
GLU
204
n
97
GLU
204
A
LYS
205
n
98
LYS
205
A
ALA
206
n
99
ALA
206
A
ASN
207
n
100
ASN
207
A
GLU
208
n
101
GLU
208
A
SER
209
n
102
SER
209
A
LEU
210
n
103
LEU
210
A
SER
211
n
104
SER
211
A
SER
212
n
105
SER
212
A
THR
213
n
106
THR
213
A
LEU
214
n
107
LEU
214
A
PRO
215
n
108
PRO
215
A
ILE
216
n
109
ILE
216
A
LEU
217
n
110
LEU
217
A
LYS
218
n
111
LYS
218
A
GLU
219
n
112
GLU
219
A
GLU
220
n
113
GLU
220
A
ILE
221
n
114
ILE
221
A
LYS
222
n
115
LYS
222
A
ASP
223
n
116
ASP
223
A
LEU
224
n
117
LEU
224
A
ASP
225
n
118
ASP
225
A
THR
226
n
119
THR
226
A
ASN
227
n
120
ASN
227
A
LEU
228
n
121
LEU
228
A
PRO
229
n
122
PRO
229
A
PRO
230
n
123
PRO
230
A
ASP
231
n
124
ASP
231
A
ILE
232
n
125
ILE
232
A
TYR
233
n
126
TYR
233
A
LYS
234
n
127
LYS
234
A
LYS
235
n
128
LYS
235
A
GLU
236
n
129
GLU
236
A
ILE
237
n
130
ILE
237
A
LEU
238
n
131
LEU
238
A
ASN
239
n
132
ASN
239
A
ILE
240
n
133
ILE
240
A
ILE
241
n
134
ILE
241
A
LYS
242
n
135
LYS
242
A
LYS
243
n
136
LYS
243
A
SER
244
n
137
SER
244
A
LYS
245
n
138
LYS
245
A
ASN
246
n
139
ASN
246
A
n
140
247
A
n
141
248
A
n
142
249
A
n
143
250
A
DT
1
n
1
DT
1
B
DT
2
n
2
DT
2
B
DT
3
n
3
DT
3
B
DG
4
n
4
DG
4
B
DT
5
n
5
DT
5
B
DG
6
n
6
DG
6
B
DG
7
n
7
DG
7
B
DG
8
n
8
DG
8
B
DA
9
n
9
DA
9
B
DT
10
n
10
DT
10
B
DT
11
n
11
DT
11
B
DT
12
n
12
DT
12
B
DC
13
n
13
DC
13
B
DA
14
n
14
DA
14
B
DT
15
n
15
DT
15
B
DG
16
n
16
DG
16
B
DA
17
n
17
DA
17
B
DT
18
n
18
DT
18
B
DG
19
n
19
DG
19
B
DA
20
n
20
DA
20
B
DA
21
n
21
DA
21
B
DA
22
n
22
DA
22
B
DC
23
n
23
DC
23
B
DG
24
n
24
DG
24
B
DA
25
n
25
DA
25
B
DG
26
n
26
DG
26
B
DA
1
n
1
DA
1
C
DA
2
n
2
DA
2
C
DA
3
n
3
DA
3
C
DC
4
n
4
DC
4
C
DT
5
n
5
DT
5
C
DC
6
n
6
DC
6
C
DG
7
n
7
DG
7
C
DT
8
n
8
DT
8
C
DT
9
n
9
DT
9
C
DT
10
n
10
DT
10
C
DC
11
n
11
DC
11
C
DA
12
n
12
DA
12
C
DT
13
n
13
DT
13
C
DC
14
n
14
DC
14
C
DA
15
n
15
DA
15
C
DT
16
n
16
DT
16
C
DG
17
n
17
DG
17
C
DA
18
n
18
DA
18
C
DA
19
n
19
DA
19
C
DA
20
n
20
DA
20
C
DT
21
n
21
DT
21
C
DC
22
n
22
DC
22
C
DC
23
n
23
DC
23
C
DC
24
n
24
DC
24
C
DA
25
n
25
DA
25
C
DC
26
n
26
DC
26
C
0.0452
-0.0086
0.0505
0.0187
-0.0427
0.1317
-0.0433
-0.2066
-0.0088
0.0741
-0.0225
0.0760
-0.1410
-0.1382
-0.0045
0.2134
-0.0070
0.0321
0.4341
0.0333
0.2570
refined
-30.1676
-30.8138
32.8952
X-RAY DIFFRACTION
0.0767
-0.0320
0.0279
0.2150
-0.0283
0.1508
0.0489
0.2339
0.0360
0.0940
-0.1034
0.0714
-0.2245
0.0617
-0.1212
0.1886
-0.0668
-0.0444
0.3965
0.0892
0.1426
refined
-20.5265
-25.2779
31.9355
X-RAY DIFFRACTION
0.3417
-0.1092
-0.1646
0.0424
0.0678
0.1070
-0.1812
0.0068
-0.0742
-0.0031
0.0561
-0.0994
-0.0309
0.1742
-0.2113
0.2558
-0.0903
-0.1154
0.4915
0.0951
0.2456
refined
-6.3790
-23.1483
38.2605
X-RAY DIFFRACTION
0.0055
0.0202
0.0100
0.0680
0.0327
0.0156
-0.0052
0.0018
-0.0056
0.0102
0.0043
0.0006
0.0075
0.0101
0.0004
1.2574
-0.1141
0.1041
1.0956
-0.0338
1.4618
refined
-0.2424
-29.7580
36.7095
X-RAY DIFFRACTION
0.1288
0.0779
0.1278
0.0794
0.1425
0.2878
-0.0574
-0.0632
-0.0399
-0.1581
-0.1709
-0.0479
0.0744
0.0254
-0.2007
0.3141
0.0009
0.0852
0.1477
0.0356
0.3095
refined
-19.1836
-38.2599
19.3835
X-RAY DIFFRACTION
0.0597
0.0149
-0.0141
0.0127
-0.0173
0.0405
0.1139
-0.1299
0.1323
-0.0498
-0.1189
-0.0609
-0.0508
0.0958
0.0038
1.4484
-0.0338
0.0005
0.4092
0.1731
1.1304
refined
-12.1932
3.0182
10.7374
X-RAY DIFFRACTION
0.0207
-0.0280
-0.0577
0.0710
0.0396
0.2715
0.0353
0.0062
0.0672
-0.0717
-0.0607
0.0491
0.0317
0.1147
0.0726
0.9445
-0.5108
0.0525
-0.1818
0.2574
1.1210
refined
-13.9341
4.0738
11.9461
X-RAY DIFFRACTION
0.0639
-0.0678
-0.1058
0.0469
0.0882
0.1432
0.0401
0.0366
-0.1453
-0.2049
-0.1618
0.1048
0.0236
0.1785
0.0000
0.3682
-0.0059
0.0471
0.2461
0.0428
0.3462
refined
-19.8440
-35.8061
20.5745
X-RAY DIFFRACTION
A
131
A
156
X-RAY DIFFRACTION
1
(CHAIN A AND RESID 131:156)
A
157
A
193
X-RAY DIFFRACTION
2
(CHAIN A AND RESID 157:193)
A
194
A
242
X-RAY DIFFRACTION
3
(CHAIN A AND RESID 194:242)
A
243
A
246
X-RAY DIFFRACTION
4
(CHAIN A AND RESID 243:246)
B
1
B
19
X-RAY DIFFRACTION
5
(CHAIN B AND RESID 1:19)
B
20
B
26
X-RAY DIFFRACTION
6
(CHAIN B AND RESID 20:26)
C
1
C
12
X-RAY DIFFRACTION
7
(CHAIN C AND RESID 1:12)
C
13
C
26
X-RAY DIFFRACTION
8
(CHAIN C AND RESID 13:26)
author_and_software_defined_assembly
PISA
3
trimeric
3490
-29
15810
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
A
CB
HIS
132
A
CB
HIS
25
0
Y
1
A
CG
HIS
132
A
CG
HIS
25
0
Y
1
A
ND1
HIS
132
A
ND1
HIS
25
0
Y
1
A
CD2
HIS
132
A
CD2
HIS
25
0
Y
1
A
CE1
HIS
132
A
CE1
HIS
25
0
Y
1
A
NE2
HIS
132
A
NE2
HIS
25
0
Y
1
A
MET
108
A
MET
1
1
Y
1
A
GLY
109
A
GLY
2
1
Y
1
A
SER
110
A
SER
3
1
Y
1
A
SER
111
A
SER
4
1
Y
1
A
HIS
112
A
HIS
5
1
Y
1
A
HIS
113
A
HIS
6
1
Y
1
A
HIS
114
A
HIS
7
1
Y
1
A
HIS
115
A
HIS
8
1
Y
1
A
HIS
116
A
HIS
9
1
Y
1
A
HIS
117
A
HIS
10
1
Y
1
A
SER
118
A
SER
11
1
Y
1
A
SER
119
A
SER
12
1
Y
1
A
GLY
120
A
GLY
13
1
Y
1
A
LEU
121
A
LEU
14
1
Y
1
A
VAL
122
A
VAL
15
1
Y
1
A
PRO
123
A
PRO
16
1
Y
1
A
ARG
124
A
ARG
17
1
Y
1
A
GLY
125
A
GLY
18
1
Y
1
A
SER
126
A
SER
19
1
Y
1
A
HIS
127
A
HIS
20
1
Y
1
A
MET
128
A
MET
21
1
Y
1
A
ALA
129
A
ALA
22
1
Y
1
A
LYS
130
A
LYS
23
1
Y
1
A
ARG
247
A
ARG
140
1
Y
1
A
LYS
248
A
LYS
141
1
Y
1
A
GLN
249
A
GLN
142
1
Y
1
A
ASN
250
A
ASN
143
1
Y
1
A
A
HZ3
O
LYS
HOH
194
327
1.56
1
A
A
O
O
HOH
HOH
302
326
1.85
1
A
B
O
O
HOH
HOH
324
103
1.89
1
A
B
O
O
HOH
HOH
307
105
2.03
1
A
A
OG
O
SER
HOH
244
304
2.04
1
A
A
OH
O
TYR
HOH
193
325
2.13
1
2.31
0.30
108.30
110.61
B
B
B
O4'
C1'
N9
DG
DG
DG
19
19
19
N
1
-6.51
0.80
102.40
95.89
C
C
C
C3'
C2'
C1'
DA
DA
DA
2
2
2
N
1
2.54
0.30
108.30
110.84
C
C
C
O4'
C1'
N9
DA
DA
DA
2
2
2
N
1
A
A
OD2
O
ASP
HOH
153
320
1.96
1_555
4_447
1
A
ASP
225
-55.21
105.80
1
A
PRO
230
-94.83
-77.15
146.180
59.6660
10.370
11.0965
-0.0000
-0.0000
-7.1143
-0.0000
-3.9822
0.2797
0.2640
0.2647
2.431
40.850
694
13893
13893
5.00
96.31
1.000
0.000
0.7913
0.46
RANDOM
1
THROUGHOUT
1.88
MOLECULAR REPLACEMENT
26.7100
0.98
1.20
PDB entry: 3VWB
ML
FLAT BULK SOLVENT MODEL
30.720
0.325
2.431
40.850
70
2061
0
1060
931
0.002
2134
0.748
3101
0.036
351
0.003
212
25.488
882
0.3778
0.3532
2.6191
136
2583
2719
5
97.0000
0.3579
0.3181
2.8826
142
2686
2828
5
100.0000
0.2874
0.2910
3.2995
140
2695
2835
5
99.0000
0.2935
0.2843
4.1564
125
2367
2492
5
87.0000
0.2245
0.2058
40.8557
151
2868
3019
5
99.0000
46.6
2.43
40.85
3W3C
13931
13895
-3.0
-3.0
0.049
0.049
1
20.49
4.95
96.6
2.43
2.58
4.77
2174
0.254
1
3.97
95.8
data collection
ADSC
Quantum
phasing
PHASER
for MR
refinement
PHENIX
(phenix.refine: 1.7.3_928)
data reduction
XDS
package
data scaling
XDS
package
Crystal structure of VirB core domain complexed with the cis-acting site upstream icsb promoter
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
4
N
N
A
SER
133
A
SER
26
HELX_P
A
LEU
141
A
LEU
34
1
1
9
A
LEU
141
A
LEU
34
HELX_P
A
VAL
146
A
VAL
39
1
2
6
A
SER
150
A
SER
43
HELX_P
A
GLU
158
A
GLU
51
1
3
9
A
SER
161
A
SER
54
HELX_P
A
SER
173
A
SER
66
1
4
13
A
PRO
175
A
PRO
68
HELX_P
A
SER
180
A
SER
73
1
5
6
A
ILE
184
A
ILE
77
HELX_P
A
LEU
188
A
LEU
81
5
6
5
A
ASN
189
A
ASN
82
HELX_P
A
ALA
206
A
ALA
99
1
7
18
A
THR
213
A
THR
106
HELX_P
A
LEU
224
A
LEU
117
1
8
12
A
ASP
231
A
ASP
124
HELX_P
A
ASN
246
A
ASN
139
1
9
16
hydrog
WATSON-CRICK
B
DG
4
B
N1
DG
4
1_555
C
DC
26
C
N3
DC
26
1_555
hydrog
WATSON-CRICK
B
DG
4
B
N2
DG
4
1_555
C
DC
26
C
O2
DC
26
1_555
hydrog
WATSON-CRICK
B
DG
4
B
O6
DG
4
1_555
C
DC
26
C
N4
DC
26
1_555
hydrog
WATSON-CRICK
B
DT
5
B
N3
DT
5
1_555
C
DA
25
C
N1
DA
25
1_555
hydrog
WATSON-CRICK
B
DT
5
B
O4
DT
5
1_555
C
DA
25
C
N6
DA
25
1_555
hydrog
WATSON-CRICK
B
DG
6
B
N1
DG
6
1_555
C
DC
24
C
N3
DC
24
1_555
hydrog
WATSON-CRICK
B
DG
6
B
N2
DG
6
1_555
C
DC
24
C
O2
DC
24
1_555
hydrog
WATSON-CRICK
B
DG
6
B
O6
DG
6
1_555
C
DC
24
C
N4
DC
24
1_555
hydrog
WATSON-CRICK
B
DG
7
B
N1
DG
7
1_555
C
DC
23
C
N3
DC
23
1_555
hydrog
WATSON-CRICK
B
DG
7
B
N2
DG
7
1_555
C
DC
23
C
O2
DC
23
1_555
hydrog
WATSON-CRICK
B
DG
7
B
O6
DG
7
1_555
C
DC
23
C
N4
DC
23
1_555
hydrog
WATSON-CRICK
B
DG
8
B
N1
DG
8
1_555
C
DC
22
C
N3
DC
22
1_555
hydrog
WATSON-CRICK
B
DG
8
B
N2
DG
8
1_555
C
DC
22
C
O2
DC
22
1_555
hydrog
WATSON-CRICK
B
DG
8
B
O6
DG
8
1_555
C
DC
22
C
N4
DC
22
1_555
hydrog
WATSON-CRICK
B
DA
9
B
N1
DA
9
1_555
C
DT
21
C
N3
DT
21
1_555
hydrog
WATSON-CRICK
B
DA
9
B
N6
DA
9
1_555
C
DT
21
C
O4
DT
21
1_555
hydrog
WATSON-CRICK
B
DT
10
B
N3
DT
10
1_555
C
DA
20
C
N1
DA
20
1_555
hydrog
WATSON-CRICK
B
DT
10
B
O4
DT
10
1_555
C
DA
20
C
N6
DA
20
1_555
hydrog
WATSON-CRICK
B
DT
11
B
N3
DT
11
1_555
C
DA
19
C
N1
DA
19
1_555
hydrog
WATSON-CRICK
B
DT
11
B
O4
DT
11
1_555
C
DA
19
C
N6
DA
19
1_555
hydrog
WATSON-CRICK
B
DT
12
B
N3
DT
12
1_555
C
DA
18
C
N1
DA
18
1_555
hydrog
WATSON-CRICK
B
DT
12
B
O4
DT
12
1_555
C
DA
18
C
N6
DA
18
1_555
hydrog
WATSON-CRICK
B
DC
13
B
N3
DC
13
1_555
C
DG
17
C
N1
DG
17
1_555
hydrog
WATSON-CRICK
B
DC
13
B
N4
DC
13
1_555
C
DG
17
C
O6
DG
17
1_555
hydrog
WATSON-CRICK
B
DC
13
B
O2
DC
13
1_555
C
DG
17
C
N2
DG
17
1_555
hydrog
WATSON-CRICK
B
DA
14
B
N1
DA
14
1_555
C
DT
16
C
N3
DT
16
1_555
hydrog
WATSON-CRICK
B
DA
14
B
N6
DA
14
1_555
C
DT
16
C
O4
DT
16
1_555
hydrog
WATSON-CRICK
B
DT
15
B
N3
DT
15
1_555
C
DA
15
C
N1
DA
15
1_555
hydrog
WATSON-CRICK
B
DT
15
B
O4
DT
15
1_555
C
DA
15
C
N6
DA
15
1_555
hydrog
WATSON-CRICK
B
DG
16
B
N1
DG
16
1_555
C
DC
14
C
N3
DC
14
1_555
hydrog
WATSON-CRICK
B
DG
16
B
N2
DG
16
1_555
C
DC
14
C
O2
DC
14
1_555
hydrog
WATSON-CRICK
B
DG
16
B
O6
DG
16
1_555
C
DC
14
C
N4
DC
14
1_555
hydrog
WATSON-CRICK
B
DA
17
B
N1
DA
17
1_555
C
DT
13
C
N3
DT
13
1_555
hydrog
WATSON-CRICK
B
DA
17
B
N6
DA
17
1_555
C
DT
13
C
O4
DT
13
1_555
hydrog
WATSON-CRICK
B
DT
18
B
N3
DT
18
1_555
C
DA
12
C
N1
DA
12
1_555
hydrog
WATSON-CRICK
B
DT
18
B
O4
DT
18
1_555
C
DA
12
C
N6
DA
12
1_555
hydrog
WATSON-CRICK
B
DG
19
B
N1
DG
19
1_555
C
DC
11
C
N3
DC
11
1_555
hydrog
WATSON-CRICK
B
DG
19
B
N2
DG
19
1_555
C
DC
11
C
O2
DC
11
1_555
hydrog
WATSON-CRICK
B
DG
19
B
O6
DG
19
1_555
C
DC
11
C
N4
DC
11
1_555
hydrog
WATSON-CRICK
B
DA
20
B
N1
DA
20
1_555
C
DT
10
C
N3
DT
10
1_555
hydrog
WATSON-CRICK
B
DA
20
B
N6
DA
20
1_555
C
DT
10
C
O4
DT
10
1_555
hydrog
WATSON-CRICK
B
DA
21
B
N1
DA
21
1_555
C
DT
9
C
N3
DT
9
1_555
hydrog
WATSON-CRICK
B
DA
21
B
N6
DA
21
1_555
C
DT
9
C
O4
DT
9
1_555
hydrog
DA-DT PAIR
B
DA
22
B
N1
DA
22
1_555
C
DT
8
C
N3
DT
8
1_555
hydrog
WATSON-CRICK
B
DC
23
B
N3
DC
23
1_555
C
DG
7
C
N1
DG
7
1_555
hydrog
WATSON-CRICK
B
DC
23
B
N4
DC
23
1_555
C
DG
7
C
O6
DG
7
1_555
hydrog
WATSON-CRICK
B
DC
23
B
O2
DC
23
1_555
C
DG
7
C
N2
DG
7
1_555
hydrog
WATSON-CRICK
B
DG
24
B
N1
DG
24
1_555
C
DC
6
C
N3
DC
6
1_555
hydrog
WATSON-CRICK
B
DG
24
B
N2
DG
24
1_555
C
DC
6
C
O2
DC
6
1_555
hydrog
WATSON-CRICK
B
DG
24
B
O6
DG
24
1_555
C
DC
6
C
N4
DC
6
1_555
hydrog
WATSON-CRICK
B
DA
25
B
N1
DA
25
1_555
C
DT
5
C
N3
DT
5
1_555
hydrog
WATSON-CRICK
B
DA
25
B
N6
DA
25
1_555
C
DT
5
C
O4
DT
5
1_555
hydrog
DG-DA MISPAIR
B
DG
26
B
O6
DG
26
1_555
C
DA
3
C
N6
DA
3
1_555
hydrog
WATSON-CRICK
B
DG
26
B
N1
DG
26
1_555
C
DC
4
C
N3
DC
4
1_555
hydrog
WATSON-CRICK
B
DG
26
B
N2
DG
26
1_555
C
DC
4
C
O2
DC
4
1_555
hydrog
WATSON-CRICK
B
DG
26
B
O6
DG
26
1_555
C
DC
4
C
N4
DC
4
1_555
TRANSCRIPTION/DNA
HTH DNA binding motif, PROTEIN-DNA COMPLEX, ParB box-A like sequence, ParB like fold, transcriptional activator, sequence specific dsDNA binding, TRANSCRIPTION-DNA complex
A
THR
226
A
THR
119
1
A
ASN
227
A
ASN
120
1.64
VIRB_SHIFL
UNP
1
129
P0A247
AKEHSIRELGIGLNFLKVSGMSYKDIAKKENLSRAKVTRAFQAASVPQEIISLFPIASELNFNDYKILFNYYKGLEKANE
SLSSTLPILKEEIKDLDTNLPPDIYKKEILNIIKKSKNRKQN
3W3C
PDB
2
3W3C
3W3C
PDB
3
3W3C
129
250
3W3C
129
250
P0A247
A
1
22
143
1
26
3W3C
1
26
3W3C
B
2
1
26
1
26
3W3C
1
26
3W3C
C
3
1
26
1
expression tag
MET
108
3W3C
A
P0A247
UNP
1
1
expression tag
GLY
109
3W3C
A
P0A247
UNP
2
1
expression tag
SER
110
3W3C
A
P0A247
UNP
3
1
expression tag
SER
111
3W3C
A
P0A247
UNP
4
1
expression tag
HIS
112
3W3C
A
P0A247
UNP
5
1
expression tag
HIS
113
3W3C
A
P0A247
UNP
6
1
expression tag
HIS
114
3W3C
A
P0A247
UNP
7
1
expression tag
HIS
115
3W3C
A
P0A247
UNP
8
1
expression tag
HIS
116
3W3C
A
P0A247
UNP
9
1
expression tag
HIS
117
3W3C
A
P0A247
UNP
10
1
expression tag
SER
118
3W3C
A
P0A247
UNP
11
1
expression tag
SER
119
3W3C
A
P0A247
UNP
12
1
expression tag
GLY
120
3W3C
A
P0A247
UNP
13
1
expression tag
LEU
121
3W3C
A
P0A247
UNP
14
1
expression tag
VAL
122
3W3C
A
P0A247
UNP
15
1
expression tag
PRO
123
3W3C
A
P0A247
UNP
16
1
expression tag
ARG
124
3W3C
A
P0A247
UNP
17
1
expression tag
GLY
125
3W3C
A
P0A247
UNP
18
1
expression tag
SER
126
3W3C
A
P0A247
UNP
19
1
expression tag
HIS
127
3W3C
A
P0A247
UNP
20
1
expression tag
MET
128
3W3C
A
P0A247
UNP
21
18
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