0.020596
0.011891
0.000000
0.000000
0.023782
0.000000
0.000000
0.000000
0.006496
0.000000
0.000000
0.000000
Fillenberg, S.B.
Muller, Y.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.000
90.000
120.000
48.554
48.554
153.941
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
Cl -1
35.453
CHLORIDE ION
non-polymer
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
CL
N
75
N
O
N
76
N
P
N
77
N
O
N
78
N
O
N
79
N
O
N
80
N
C
N
81
R
C
N
82
N
O
N
83
S
C
N
84
N
O
N
85
N
C
N
86
R
C
Y
87
N
N
Y
88
N
C
Y
89
N
N
Y
90
N
C
Y
91
N
C
N
92
N
N
Y
93
N
N
Y
94
N
C
Y
95
N
N
Y
96
N
C
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
H
N
111
N
O
N
112
N
P
N
113
N
O
N
114
N
O
N
115
N
O
N
116
N
C
N
117
R
C
N
118
N
O
N
119
S
C
N
120
N
O
N
121
N
C
N
122
R
C
N
123
N
N
N
124
N
C
N
125
N
O
N
126
N
N
N
127
N
C
N
128
N
N
N
129
N
C
N
130
N
C
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
H
N
145
N
O
N
146
N
P
N
147
N
O
N
148
N
O
N
149
N
O
N
150
N
C
N
151
R
C
N
152
N
O
N
153
S
C
N
154
N
O
N
155
N
C
N
156
R
C
Y
157
N
N
Y
158
N
C
Y
159
N
N
Y
160
N
C
N
161
N
C
N
162
N
O
N
163
N
N
N
164
N
C
N
165
N
N
N
166
N
N
Y
167
N
C
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
H
N
182
N
O
N
183
N
P
N
184
N
O
N
185
N
O
N
186
N
O
N
187
N
C
N
188
R
C
N
189
N
O
N
190
S
C
N
191
N
O
N
192
N
C
N
193
R
C
N
194
N
N
N
195
N
C
N
196
N
O
N
197
N
N
N
198
N
C
N
199
N
O
N
200
N
C
N
201
N
C
N
202
N
C
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
H
N
218
N
N
N
219
S
C
N
220
N
C
N
221
N
O
N
222
N
C
N
223
N
C
N
224
N
C
N
225
N
O
N
226
N
N
N
227
N
O
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
H
N
238
N
N
N
239
S
C
N
240
N
C
N
241
N
O
N
242
N
C
N
243
N
C
N
244
N
C
N
245
N
O
N
246
N
O
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
N
N
258
N
C
N
259
N
C
N
260
N
O
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
N
N
268
S
C
N
269
N
C
N
270
N
O
N
271
N
C
Y
272
N
C
Y
273
N
N
Y
274
N
C
Y
275
N
C
Y
276
N
N
N
277
N
O
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
H
N
288
N
O
N
289
N
H
N
290
N
H
N
291
N
N
N
292
S
C
N
293
N
C
N
294
N
O
N
295
S
C
N
296
N
C
N
297
N
C
N
298
N
C
N
299
N
O
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
H
N
313
N
N
N
314
S
C
N
315
N
C
N
316
N
O
N
317
N
C
N
318
N
C
N
319
N
C
N
320
N
C
N
321
N
O
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
H
N
335
N
N
N
336
S
C
N
337
N
C
N
338
N
O
N
339
N
C
N
340
N
C
N
341
N
C
N
342
N
C
N
343
N
N
N
344
N
O
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
H
N
360
N
N
N
361
S
C
N
362
N
C
N
363
N
O
N
364
N
C
N
365
N
C
N
366
N
S
N
367
N
C
N
368
N
O
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
H
N
380
N
N
N
381
S
C
N
382
N
C
N
383
N
O
N
384
N
C
Y
385
N
C
Y
386
N
C
Y
387
N
C
Y
388
N
C
Y
389
N
C
Y
390
N
C
N
391
N
O
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
H
N
403
N
N
N
404
S
C
N
405
N
C
N
406
N
O
N
407
N
C
N
408
N
C
N
409
N
C
N
410
N
O
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
H
N
420
N
N
N
421
S
C
N
422
N
C
N
423
N
O
N
424
N
C
N
425
N
O
N
426
N
O
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
H
N
434
N
N
N
435
S
C
N
436
N
C
N
437
N
O
N
438
R
C
N
439
N
O
N
440
N
C
N
441
N
O
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
H
N
451
N
N
N
452
S
C
N
453
N
C
N
454
N
O
N
455
N
C
Y
456
N
C
Y
457
N
C
Y
458
N
C
Y
459
N
C
Y
460
N
C
Y
461
N
C
N
462
N
O
N
463
N
O
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
H
N
475
N
N
N
476
S
C
N
477
N
C
N
478
N
O
N
479
N
C
N
480
N
C
N
481
N
C
N
482
N
O
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
493
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
1362-4962
43
1283
1296
10.1093/nar/gku1374
25564531
Structural insight into operator dre-sites recognition and effector binding in the GntR/HutC transcription regulator NagR.
2015
10.2210/pdb4u0y/pdb
pdb_00004u0y
100
1
CCD
2010-10-08
RAYONIX MX-225
Si-111 crystal
SINGLE WAVELENGTH
M
x-ray
1
0.91841
1.0
14.1
BESSY
0.91841
SYNCHROTRON
BESSY BEAMLINE 14.1
Truncated form of YvoA; comprises only the DNA-binding domain (residues 1-75)
8965.283
HTH-type transcriptional repressor YvoA
UNP residues 1-75
4
man
polymer
15mer palindromic dsDNA construct; derived from the consensus sequence of the two native non-palindromic dre-site sequences upstream of nagAB-yvoA and nagP
4584.984
DNA (5'-D(P*GP*TP*GP*GP*TP*CP*TP*AP*GP*AP*CP*CP*AP*CP*T)-3')
2
syn
polymer
35.453
CHLORIDE ION
2
syn
non-polymer
18.015
water
287
nat
water
no
no
GSHMNINKQSPIPIYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGRGTFVS
GSHMNINKQSPIPIYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGRGTFVS
A,B,C,D
polypeptide(L)
no
no
(DG)(DT)(DG)(DG)(DT)(DC)(DT)(DA)(DG)(DA)(DC)(DC)(DA)(DC)(DT)
GTGGTCTAGACCACT
E,F
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
sample
1
78
yvoA, BSU35030
224308
Bacillus subtilis subsp. subtilis str. 168
562
Escherichia coli
Biological sequence
1
2.39
48.46
VAPOR DIFFUSION, SITTING DROP
6.5
50 mM sodium cacodylate,
200 mM sodium citrate,
10 mM MgCl2,
5 % (v/v) isopropanol
292.15
7.425
1
19
E
1
F
14
-0.144
E_DG1:DC14_F
1
12.082
-0.189
-0.086
-0.113
5.541
1
20
E
2
F
13
-0.206
E_DT2:DA13_F
2
-10.432
-0.091
0.369
-0.146
12.804
1
19
E
3
F
12
-1.043
E_DG3:DC12_F
3
-3.971
-0.075
0.447
-0.081
-11.730
1
19
E
4
F
11
0.093
E_DG4:DC11_F
4
-9.181
-0.385
-0.387
-0.220
1.574
1
20
E
5
F
10
2.586
E_DT5:DA10_F
5
-12.566
-0.188
0.079
-0.117
-2.520
1
19
E
6
F
9
0.032
E_DC6:DG9_F
6
-8.568
0.101
0.168
-0.048
-2.670
1
20
E
7
F
8
3.099
E_DT7:DA8_F
7
-8.794
-0.070
-0.336
-0.092
4.209
1
20
E
8
F
7
2.881
E_DA8:DT7_F
8
-8.632
0.266
-0.211
-0.081
2.212
1
19
E
9
F
6
0.789
E_DG9:DC6_F
9
-7.310
-0.138
0.113
-0.042
-0.478
1
20
E
10
F
5
4.897
E_DA10:DT5_F
10
-15.120
0.193
0.101
-0.046
12.499
1
19
E
11
F
4
2.777
E_DC11:DG4_F
11
-7.797
0.314
-0.526
-0.096
-10.340
1
19
E
12
F
3
0.372
E_DC12:DG3_F
12
-4.078
0.154
0.141
-0.141
-9.643
1
20
E
13
F
2
1.761
E_DA13:DT2_F
13
-12.457
0.029
0.134
-0.179
-9.416
1
19
E
14
F
1
0.772
E_DC14:DG1_F
14
16.606
0.142
-0.073
-0.086
3.628
32.383
E
E
1
2
-11.517
F
F
14
13
3.525
-6.377
-0.871
-0.581
EE_DG1DT2:DA13DC14_FF
1
-2.597
4.690
31.662
0.202
1.055
3.016
36.962
E
E
2
3
5.430
F
F
13
12
3.037
3.437
0.396
-0.193
EE_DT2DG3:DC12DA13_FF
2
0.939
-1.483
36.796
-0.734
-0.508
3.769
39.525
E
E
3
4
3.726
F
F
12
11
3.889
2.509
0.065
-1.305
EE_DG3DG4:DC11DC12_FF
3
6.077
-9.025
38.996
-2.277
0.746
2.781
32.262
E
E
4
5
8.056
F
F
11
10
2.969
4.448
0.290
-0.658
EE_DG4DT5:DA10DC11_FF
4
-4.738
8.583
31.617
-1.886
-1.269
3.464
34.613
E
E
5
6
-0.785
F
F
10
9
3.472
-0.467
0.326
-1.131
EE_DT5DC6:DG9DA10_FF
5
-1.894
3.184
34.560
-1.825
-0.858
2.924
25.846
E
E
6
7
4.289
F
F
9
8
3.256
1.903
-0.925
-0.862
EE_DC6DT7:DA8DG9_FF
6
5.418
-12.211
25.211
-2.434
3.510
3.491
29.784
E
E
7
8
37.889
F
F
8
7
3.547
18.156
-0.106
1.091
EE_DT7DA8:DT7DA8_FF
7
-1.253
2.615
23.677
-2.452
-0.110
3.177
24.753
E
E
8
9
0.754
F
F
7
6
3.386
0.322
0.977
-0.825
EE_DA8DG9:DC6DT7_FF
8
-3.988
9.342
24.433
-2.022
-3.501
3.417
35.464
E
E
9
10
-0.579
F
F
6
5
3.433
-0.353
-0.311
-1.092
EE_DG9DA10:DT5DC6_FF
9
2.305
-3.786
35.390
-1.739
0.865
2.717
31.623
E
E
10
11
11.466
F
F
5
4
2.963
6.181
-0.258
-0.572
EE_DA10DC11:DG4DT5_FF
10
5.277
-9.788
30.587
-2.061
1.336
3.736
39.785
E
E
11
12
4.324
F
F
4
3
3.835
2.931
-0.202
-1.174
EE_DC11DC12:DG3DG4_FF
11
-5.401
7.966
39.327
-2.121
-0.432
3.218
36.312
E
E
12
13
9.459
F
F
3
2
3.241
5.869
-0.419
0.006
EE_DC12DA13:DT2DG3_FF
12
-1.741
2.805
35.809
-0.805
0.431
3.544
34.118
E
E
13
14
-14.402
F
F
2
1
3.526
-8.369
0.826
-0.504
EE_DA13DC14:DG1DT2_FF
13
-0.035
0.061
33.105
0.599
-1.414
atom_site
chem_comp_atom
chem_comp_bond
database_2
ndb_struct_na_base_pair
ndb_struct_na_base_pair_step
pdbx_audit_support
pdbx_initial_refinement_model
pdbx_nonpoly_scheme
pdbx_validate_close_contact
struct_site_gen
repository
Initial release
Database references
Database references
Advisory
Atomic model
Author supporting evidence
Data collection
Database references
Derived calculations
Refinement description
1
0
2015-01-14
1
1
2015-01-21
1
2
2015-02-04
2
0
2023-12-20
_atom_site.B_iso_or_equiv
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_ndb_struct_na_base_pair.propeller
_ndb_struct_na_base_pair_step.inclination
_ndb_struct_na_base_pair_step.roll
_ndb_struct_na_base_pair_step.tip
_pdbx_audit_support.funding_organization
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_validate_close_contact.auth_seq_id_1
_pdbx_validate_close_contact.auth_seq_id_2
_struct_site_gen.auth_seq_id
Germany
German Research Foundation
N
RCSB
Y
PDBE
2014-07-14
REL
REL
CL
CHLORIDE ION
HOH
water
224308
Bacillus subtilis subsp. subtilis str. 168
sample
1
15
2WV0
DNA-binding domain of PDB entry 2wv0
PDB
experimental model
CL
1
3
CL
CL
101
B
CL
1
3
CL
CL
101
C
HOH
168
4
HOH
HOH
101
A
HOH
188
4
HOH
HOH
102
A
HOH
204
4
HOH
HOH
103
A
HOH
281
4
HOH
HOH
104
A
HOH
180
4
HOH
HOH
105
A
HOH
62
4
HOH
HOH
106
A
HOH
238
4
HOH
HOH
107
A
HOH
256
4
HOH
HOH
108
A
HOH
83
4
HOH
HOH
109
A
HOH
101
4
HOH
HOH
110
A
HOH
202
4
HOH
HOH
111
A
HOH
28
4
HOH
HOH
112
A
HOH
130
4
HOH
HOH
113
A
HOH
37
4
HOH
HOH
114
A
HOH
16
4
HOH
HOH
115
A
HOH
105
4
HOH
HOH
116
A
HOH
158
4
HOH
HOH
117
A
HOH
183
4
HOH
HOH
118
A
HOH
167
4
HOH
HOH
119
A
HOH
103
4
HOH
HOH
120
A
HOH
65
4
HOH
HOH
121
A
HOH
199
4
HOH
HOH
122
A
HOH
60
4
HOH
HOH
123
A
HOH
209
4
HOH
HOH
124
A
HOH
112
4
HOH
HOH
125
A
HOH
252
4
HOH
HOH
126
A
HOH
39
4
HOH
HOH
127
A
HOH
72
4
HOH
HOH
128
A
HOH
156
4
HOH
HOH
129
A
HOH
178
4
HOH
HOH
130
A
HOH
261
4
HOH
HOH
131
A
HOH
200
4
HOH
HOH
132
A
HOH
122
4
HOH
HOH
133
A
HOH
160
4
HOH
HOH
134
A
HOH
95
4
HOH
HOH
135
A
HOH
111
4
HOH
HOH
136
A
HOH
121
4
HOH
HOH
137
A
HOH
186
4
HOH
HOH
138
A
HOH
77
4
HOH
HOH
139
A
HOH
49
4
HOH
HOH
140
A
HOH
58
4
HOH
HOH
141
A
HOH
288
4
HOH
HOH
142
A
HOH
219
4
HOH
HOH
143
A
HOH
262
4
HOH
HOH
144
A
HOH
157
4
HOH
HOH
145
A
HOH
173
4
HOH
HOH
146
A
HOH
221
4
HOH
HOH
147
A
HOH
226
4
HOH
HOH
148
A
HOH
148
4
HOH
HOH
201
B
HOH
218
4
HOH
HOH
202
B
HOH
134
4
HOH
HOH
203
B
HOH
97
4
HOH
HOH
204
B
HOH
271
4
HOH
HOH
205
B
HOH
22
4
HOH
HOH
206
B
HOH
86
4
HOH
HOH
207
B
HOH
224
4
HOH
HOH
208
B
HOH
237
4
HOH
HOH
209
B
HOH
165
4
HOH
HOH
210
B
HOH
266
4
HOH
HOH
211
B
HOH
109
4
HOH
HOH
212
B
HOH
53
4
HOH
HOH
213
B
HOH
57
4
HOH
HOH
214
B
HOH
215
4
HOH
HOH
215
B
HOH
36
4
HOH
HOH
216
B
HOH
98
4
HOH
HOH
217
B
HOH
151
4
HOH
HOH
218
B
HOH
117
4
HOH
HOH
219
B
HOH
68
4
HOH
HOH
220
B
HOH
76
4
HOH
HOH
221
B
HOH
192
4
HOH
HOH
222
B
HOH
147
4
HOH
HOH
223
B
HOH
106
4
HOH
HOH
224
B
HOH
34
4
HOH
HOH
225
B
HOH
23
4
HOH
HOH
226
B
HOH
236
4
HOH
HOH
227
B
HOH
85
4
HOH
HOH
228
B
HOH
43
4
HOH
HOH
229
B
HOH
115
4
HOH
HOH
230
B
HOH
216
4
HOH
HOH
231
B
HOH
133
4
HOH
HOH
232
B
HOH
129
4
HOH
HOH
233
B
HOH
14
4
HOH
HOH
234
B
HOH
172
4
HOH
HOH
235
B
HOH
175
4
HOH
HOH
236
B
HOH
54
4
HOH
HOH
237
B
HOH
189
4
HOH
HOH
238
B
HOH
197
4
HOH
HOH
239
B
HOH
211
4
HOH
HOH
240
B
HOH
250
4
HOH
HOH
241
B
HOH
280
4
HOH
HOH
242
B
HOH
114
4
HOH
HOH
243
B
HOH
228
4
HOH
HOH
244
B
HOH
205
4
HOH
HOH
245
B
HOH
227
4
HOH
HOH
246
B
HOH
126
4
HOH
HOH
247
B
HOH
29
4
HOH
HOH
248
B
HOH
214
4
HOH
HOH
249
B
HOH
260
4
HOH
HOH
250
B
HOH
283
4
HOH
HOH
251
B
HOH
245
4
HOH
HOH
252
B
HOH
289
4
HOH
HOH
253
B
HOH
164
4
HOH
HOH
201
C
HOH
229
4
HOH
HOH
202
C
HOH
174
4
HOH
HOH
203
C
HOH
230
4
HOH
HOH
204
C
HOH
146
4
HOH
HOH
205
C
HOH
241
4
HOH
HOH
206
C
HOH
203
4
HOH
HOH
207
C
HOH
213
4
HOH
HOH
208
C
HOH
99
4
HOH
HOH
209
C
HOH
234
4
HOH
HOH
210
C
HOH
152
4
HOH
HOH
211
C
HOH
196
4
HOH
HOH
212
C
HOH
90
4
HOH
HOH
213
C
HOH
142
4
HOH
HOH
214
C
HOH
104
4
HOH
HOH
215
C
HOH
286
4
HOH
HOH
216
C
HOH
181
4
HOH
HOH
217
C
HOH
136
4
HOH
HOH
218
C
HOH
161
4
HOH
HOH
219
C
HOH
169
4
HOH
HOH
220
C
HOH
193
4
HOH
HOH
221
C
HOH
79
4
HOH
HOH
222
C
HOH
233
4
HOH
HOH
223
C
HOH
35
4
HOH
HOH
224
C
HOH
223
4
HOH
HOH
225
C
HOH
210
4
HOH
HOH
226
C
HOH
206
4
HOH
HOH
227
C
HOH
253
4
HOH
HOH
228
C
HOH
84
4
HOH
HOH
229
C
HOH
138
4
HOH
HOH
230
C
HOH
124
4
HOH
HOH
231
C
HOH
89
4
HOH
HOH
232
C
HOH
208
4
HOH
HOH
233
C
HOH
171
4
HOH
HOH
234
C
HOH
254
4
HOH
HOH
235
C
HOH
52
4
HOH
HOH
236
C
HOH
70
4
HOH
HOH
237
C
HOH
225
4
HOH
HOH
238
C
HOH
61
4
HOH
HOH
239
C
HOH
232
4
HOH
HOH
240
C
HOH
187
4
HOH
HOH
241
C
HOH
59
4
HOH
HOH
242
C
HOH
153
4
HOH
HOH
243
C
HOH
272
4
HOH
HOH
244
C
HOH
201
4
HOH
HOH
245
C
HOH
170
4
HOH
HOH
246
C
HOH
269
4
HOH
HOH
247
C
HOH
258
4
HOH
HOH
248
C
HOH
276
4
HOH
HOH
249
C
HOH
282
4
HOH
HOH
250
C
HOH
287
4
HOH
HOH
251
C
HOH
265
4
HOH
HOH
252
C
HOH
149
4
HOH
HOH
101
D
HOH
182
4
HOH
HOH
102
D
HOH
108
4
HOH
HOH
103
D
HOH
274
4
HOH
HOH
104
D
HOH
244
4
HOH
HOH
105
D
HOH
110
4
HOH
HOH
106
D
HOH
127
4
HOH
HOH
107
D
HOH
128
4
HOH
HOH
108
D
HOH
67
4
HOH
HOH
109
D
HOH
240
4
HOH
HOH
110
D
HOH
235
4
HOH
HOH
111
D
HOH
7
4
HOH
HOH
112
D
HOH
125
4
HOH
HOH
113
D
HOH
74
4
HOH
HOH
114
D
HOH
143
4
HOH
HOH
115
D
HOH
177
4
HOH
HOH
116
D
HOH
31
4
HOH
HOH
117
D
HOH
273
4
HOH
HOH
118
D
HOH
155
4
HOH
HOH
119
D
HOH
163
4
HOH
HOH
120
D
HOH
166
4
HOH
HOH
121
D
HOH
11
4
HOH
HOH
122
D
HOH
51
4
HOH
HOH
123
D
HOH
140
4
HOH
HOH
124
D
HOH
19
4
HOH
HOH
125
D
HOH
264
4
HOH
HOH
126
D
HOH
145
4
HOH
HOH
127
D
HOH
284
4
HOH
HOH
128
D
HOH
50
4
HOH
HOH
129
D
HOH
107
4
HOH
HOH
130
D
HOH
285
4
HOH
HOH
131
D
HOH
176
4
HOH
HOH
132
D
HOH
137
4
HOH
HOH
133
D
HOH
135
4
HOH
HOH
134
D
HOH
6
4
HOH
HOH
135
D
HOH
278
4
HOH
HOH
136
D
HOH
123
4
HOH
HOH
101
E
HOH
162
4
HOH
HOH
102
E
HOH
277
4
HOH
HOH
103
E
HOH
118
4
HOH
HOH
104
E
HOH
24
4
HOH
HOH
105
E
HOH
33
4
HOH
HOH
106
E
HOH
44
4
HOH
HOH
107
E
HOH
13
4
HOH
HOH
108
E
HOH
46
4
HOH
HOH
109
E
HOH
8
4
HOH
HOH
110
E
HOH
116
4
HOH
HOH
111
E
HOH
63
4
HOH
HOH
112
E
HOH
212
4
HOH
HOH
113
E
HOH
257
4
HOH
HOH
114
E
HOH
73
4
HOH
HOH
115
E
HOH
194
4
HOH
HOH
116
E
HOH
18
4
HOH
HOH
117
E
HOH
132
4
HOH
HOH
118
E
HOH
195
4
HOH
HOH
119
E
HOH
154
4
HOH
HOH
120
E
HOH
26
4
HOH
HOH
121
E
HOH
255
4
HOH
HOH
122
E
HOH
25
4
HOH
HOH
123
E
HOH
248
4
HOH
HOH
124
E
HOH
45
4
HOH
HOH
125
E
HOH
48
4
HOH
HOH
126
E
HOH
190
4
HOH
HOH
127
E
HOH
15
4
HOH
HOH
128
E
HOH
3
4
HOH
HOH
129
E
HOH
27
4
HOH
HOH
130
E
HOH
21
4
HOH
HOH
131
E
HOH
32
4
HOH
HOH
132
E
HOH
4
4
HOH
HOH
133
E
HOH
87
4
HOH
HOH
134
E
HOH
75
4
HOH
HOH
135
E
HOH
222
4
HOH
HOH
136
E
HOH
207
4
HOH
HOH
137
E
HOH
81
4
HOH
HOH
138
E
HOH
263
4
HOH
HOH
139
E
HOH
100
4
HOH
HOH
140
E
HOH
131
4
HOH
HOH
141
E
HOH
150
4
HOH
HOH
142
E
HOH
94
4
HOH
HOH
143
E
HOH
80
4
HOH
HOH
144
E
HOH
91
4
HOH
HOH
145
E
HOH
96
4
HOH
HOH
146
E
HOH
139
4
HOH
HOH
147
E
HOH
251
4
HOH
HOH
101
F
HOH
267
4
HOH
HOH
102
F
HOH
242
4
HOH
HOH
103
F
HOH
239
4
HOH
HOH
104
F
HOH
249
4
HOH
HOH
105
F
HOH
47
4
HOH
HOH
106
F
HOH
10
4
HOH
HOH
107
F
HOH
184
4
HOH
HOH
108
F
HOH
185
4
HOH
HOH
109
F
HOH
66
4
HOH
HOH
110
F
HOH
141
4
HOH
HOH
111
F
HOH
78
4
HOH
HOH
112
F
HOH
9
4
HOH
HOH
113
F
HOH
42
4
HOH
HOH
114
F
HOH
82
4
HOH
HOH
115
F
HOH
93
4
HOH
HOH
116
F
HOH
92
4
HOH
HOH
117
F
HOH
120
4
HOH
HOH
118
F
HOH
243
4
HOH
HOH
119
F
HOH
198
4
HOH
HOH
120
F
HOH
12
4
HOH
HOH
121
F
HOH
38
4
HOH
HOH
122
F
HOH
247
4
HOH
HOH
123
F
HOH
41
4
HOH
HOH
124
F
HOH
279
4
HOH
HOH
125
F
HOH
55
4
HOH
HOH
126
F
HOH
20
4
HOH
HOH
127
F
HOH
159
4
HOH
HOH
128
F
HOH
30
4
HOH
HOH
129
F
HOH
71
4
HOH
HOH
130
F
HOH
5
4
HOH
HOH
131
F
HOH
17
4
HOH
HOH
132
F
HOH
69
4
HOH
HOH
133
F
HOH
56
4
HOH
HOH
134
F
HOH
64
4
HOH
HOH
135
F
HOH
40
4
HOH
HOH
136
F
HOH
259
4
HOH
HOH
137
F
HOH
144
4
HOH
HOH
138
F
HOH
191
4
HOH
HOH
139
F
HOH
102
4
HOH
HOH
140
F
HOH
179
4
HOH
HOH
141
F
HOH
217
4
HOH
HOH
142
F
HOH
119
4
HOH
HOH
143
F
HOH
220
4
HOH
HOH
144
F
HOH
246
4
HOH
HOH
145
F
HOH
268
4
HOH
HOH
146
F
HOH
88
4
HOH
HOH
147
F
HOH
231
4
HOH
HOH
148
F
HOH
113
4
HOH
HOH
149
F
HOH
270
4
HOH
HOH
150
F
HOH
275
4
HOH
HOH
151
F
n
1
-2
A
n
2
-1
A
n
3
0
A
MET
1
n
4
MET
1
A
ASN
2
n
5
ASN
2
A
ILE
3
n
6
ILE
3
A
ASN
4
n
7
ASN
4
A
LYS
5
n
8
LYS
5
A
GLN
6
n
9
GLN
6
A
SER
7
n
10
SER
7
A
PRO
8
n
11
PRO
8
A
ILE
9
n
12
ILE
9
A
PRO
10
n
13
PRO
10
A
ILE
11
n
14
ILE
11
A
TYR
12
n
15
TYR
12
A
TYR
13
n
16
TYR
13
A
GLN
14
n
17
GLN
14
A
ILE
15
n
18
ILE
15
A
MET
16
n
19
MET
16
A
GLU
17
n
20
GLU
17
A
GLN
18
n
21
GLN
18
A
LEU
19
n
22
LEU
19
A
LYS
20
n
23
LYS
20
A
THR
21
n
24
THR
21
A
GLN
22
n
25
GLN
22
A
ILE
23
n
26
ILE
23
A
LYS
24
n
27
LYS
24
A
ASN
25
n
28
ASN
25
A
GLY
26
n
29
GLY
26
A
GLU
27
n
30
GLU
27
A
LEU
28
n
31
LEU
28
A
GLN
29
n
32
GLN
29
A
PRO
30
n
33
PRO
30
A
ASP
31
n
34
ASP
31
A
MET
32
n
35
MET
32
A
PRO
33
n
36
PRO
33
A
LEU
34
n
37
LEU
34
A
PRO
35
n
38
PRO
35
A
SER
36
n
39
SER
36
A
GLU
37
n
40
GLU
37
A
ARG
38
n
41
ARG
38
A
GLU
39
n
42
GLU
39
A
TYR
40
n
43
TYR
40
A
ALA
41
n
44
ALA
41
A
GLU
42
n
45
GLU
42
A
GLN
43
n
46
GLN
43
A
PHE
44
n
47
PHE
44
A
GLY
45
n
48
GLY
45
A
ILE
46
n
49
ILE
46
A
SER
47
n
50
SER
47
A
ARG
48
n
51
ARG
48
A
MET
49
n
52
MET
49
A
THR
50
n
53
THR
50
A
VAL
51
n
54
VAL
51
A
ARG
52
n
55
ARG
52
A
GLN
53
n
56
GLN
53
A
ALA
54
n
57
ALA
54
A
LEU
55
n
58
LEU
55
A
SER
56
n
59
SER
56
A
ASN
57
n
60
ASN
57
A
LEU
58
n
61
LEU
58
A
VAL
59
n
62
VAL
59
A
ASN
60
n
63
ASN
60
A
GLU
61
n
64
GLU
61
A
GLY
62
n
65
GLY
62
A
LEU
63
n
66
LEU
63
A
LEU
64
n
67
LEU
64
A
TYR
65
n
68
TYR
65
A
ARG
66
n
69
ARG
66
A
LEU
67
n
70
LEU
67
A
LYS
68
n
71
LYS
68
A
GLY
69
n
72
GLY
69
A
ARG
70
n
73
ARG
70
A
GLY
71
n
74
GLY
71
A
THR
72
n
75
THR
72
A
PHE
73
n
76
PHE
73
A
VAL
74
n
77
VAL
74
A
SER
75
n
78
SER
75
A
n
1
-2
B
n
2
-1
B
n
3
0
B
MET
1
n
4
MET
1
B
ASN
2
n
5
ASN
2
B
ILE
3
n
6
ILE
3
B
ASN
4
n
7
ASN
4
B
LYS
5
n
8
LYS
5
B
GLN
6
n
9
GLN
6
B
SER
7
n
10
SER
7
B
PRO
8
n
11
PRO
8
B
ILE
9
n
12
ILE
9
B
PRO
10
n
13
PRO
10
B
ILE
11
n
14
ILE
11
B
TYR
12
n
15
TYR
12
B
TYR
13
n
16
TYR
13
B
GLN
14
n
17
GLN
14
B
ILE
15
n
18
ILE
15
B
MET
16
n
19
MET
16
B
GLU
17
n
20
GLU
17
B
GLN
18
n
21
GLN
18
B
LEU
19
n
22
LEU
19
B
LYS
20
n
23
LYS
20
B
THR
21
n
24
THR
21
B
GLN
22
n
25
GLN
22
B
ILE
23
n
26
ILE
23
B
LYS
24
n
27
LYS
24
B
ASN
25
n
28
ASN
25
B
GLY
26
n
29
GLY
26
B
GLU
27
n
30
GLU
27
B
LEU
28
n
31
LEU
28
B
GLN
29
n
32
GLN
29
B
PRO
30
n
33
PRO
30
B
ASP
31
n
34
ASP
31
B
MET
32
n
35
MET
32
B
PRO
33
n
36
PRO
33
B
LEU
34
n
37
LEU
34
B
PRO
35
n
38
PRO
35
B
SER
36
n
39
SER
36
B
GLU
37
n
40
GLU
37
B
ARG
38
n
41
ARG
38
B
GLU
39
n
42
GLU
39
B
TYR
40
n
43
TYR
40
B
ALA
41
n
44
ALA
41
B
GLU
42
n
45
GLU
42
B
GLN
43
n
46
GLN
43
B
PHE
44
n
47
PHE
44
B
GLY
45
n
48
GLY
45
B
ILE
46
n
49
ILE
46
B
SER
47
n
50
SER
47
B
ARG
48
n
51
ARG
48
B
MET
49
n
52
MET
49
B
THR
50
n
53
THR
50
B
VAL
51
n
54
VAL
51
B
ARG
52
n
55
ARG
52
B
GLN
53
n
56
GLN
53
B
ALA
54
n
57
ALA
54
B
LEU
55
n
58
LEU
55
B
SER
56
n
59
SER
56
B
ASN
57
n
60
ASN
57
B
LEU
58
n
61
LEU
58
B
VAL
59
n
62
VAL
59
B
ASN
60
n
63
ASN
60
B
GLU
61
n
64
GLU
61
B
GLY
62
n
65
GLY
62
B
LEU
63
n
66
LEU
63
B
LEU
64
n
67
LEU
64
B
TYR
65
n
68
TYR
65
B
ARG
66
n
69
ARG
66
B
LEU
67
n
70
LEU
67
B
LYS
68
n
71
LYS
68
B
GLY
69
n
72
GLY
69
B
ARG
70
n
73
ARG
70
B
GLY
71
n
74
GLY
71
B
THR
72
n
75
THR
72
B
PHE
73
n
76
PHE
73
B
VAL
74
n
77
VAL
74
B
SER
75
n
78
SER
75
B
n
1
-2
C
n
2
-1
C
n
3
0
C
MET
1
n
4
MET
1
C
ASN
2
n
5
ASN
2
C
ILE
3
n
6
ILE
3
C
ASN
4
n
7
ASN
4
C
LYS
5
n
8
LYS
5
C
GLN
6
n
9
GLN
6
C
SER
7
n
10
SER
7
C
PRO
8
n
11
PRO
8
C
ILE
9
n
12
ILE
9
C
PRO
10
n
13
PRO
10
C
ILE
11
n
14
ILE
11
C
TYR
12
n
15
TYR
12
C
TYR
13
n
16
TYR
13
C
GLN
14
n
17
GLN
14
C
ILE
15
n
18
ILE
15
C
MET
16
n
19
MET
16
C
GLU
17
n
20
GLU
17
C
GLN
18
n
21
GLN
18
C
LEU
19
n
22
LEU
19
C
LYS
20
n
23
LYS
20
C
THR
21
n
24
THR
21
C
GLN
22
n
25
GLN
22
C
ILE
23
n
26
ILE
23
C
LYS
24
n
27
LYS
24
C
ASN
25
n
28
ASN
25
C
GLY
26
n
29
GLY
26
C
GLU
27
n
30
GLU
27
C
LEU
28
n
31
LEU
28
C
GLN
29
n
32
GLN
29
C
PRO
30
n
33
PRO
30
C
ASP
31
n
34
ASP
31
C
MET
32
n
35
MET
32
C
PRO
33
n
36
PRO
33
C
LEU
34
n
37
LEU
34
C
PRO
35
n
38
PRO
35
C
SER
36
n
39
SER
36
C
GLU
37
n
40
GLU
37
C
ARG
38
n
41
ARG
38
C
GLU
39
n
42
GLU
39
C
TYR
40
n
43
TYR
40
C
ALA
41
n
44
ALA
41
C
GLU
42
n
45
GLU
42
C
GLN
43
n
46
GLN
43
C
PHE
44
n
47
PHE
44
C
GLY
45
n
48
GLY
45
C
ILE
46
n
49
ILE
46
C
SER
47
n
50
SER
47
C
ARG
48
n
51
ARG
48
C
MET
49
n
52
MET
49
C
THR
50
n
53
THR
50
C
VAL
51
n
54
VAL
51
C
ARG
52
n
55
ARG
52
C
GLN
53
n
56
GLN
53
C
ALA
54
n
57
ALA
54
C
LEU
55
n
58
LEU
55
C
SER
56
n
59
SER
56
C
ASN
57
n
60
ASN
57
C
LEU
58
n
61
LEU
58
C
VAL
59
n
62
VAL
59
C
ASN
60
n
63
ASN
60
C
GLU
61
n
64
GLU
61
C
GLY
62
n
65
GLY
62
C
LEU
63
n
66
LEU
63
C
LEU
64
n
67
LEU
64
C
TYR
65
n
68
TYR
65
C
ARG
66
n
69
ARG
66
C
LEU
67
n
70
LEU
67
C
LYS
68
n
71
LYS
68
C
GLY
69
n
72
GLY
69
C
ARG
70
n
73
ARG
70
C
GLY
71
n
74
GLY
71
C
THR
72
n
75
THR
72
C
PHE
73
n
76
PHE
73
C
VAL
74
n
77
VAL
74
C
SER
75
n
78
SER
75
C
n
1
-2
D
n
2
-1
D
n
3
0
D
n
4
1
D
ASN
2
n
5
ASN
2
D
ILE
3
n
6
ILE
3
D
ASN
4
n
7
ASN
4
D
LYS
5
n
8
LYS
5
D
GLN
6
n
9
GLN
6
D
SER
7
n
10
SER
7
D
PRO
8
n
11
PRO
8
D
ILE
9
n
12
ILE
9
D
PRO
10
n
13
PRO
10
D
ILE
11
n
14
ILE
11
D
TYR
12
n
15
TYR
12
D
TYR
13
n
16
TYR
13
D
GLN
14
n
17
GLN
14
D
ILE
15
n
18
ILE
15
D
MET
16
n
19
MET
16
D
GLU
17
n
20
GLU
17
D
GLN
18
n
21
GLN
18
D
LEU
19
n
22
LEU
19
D
LYS
20
n
23
LYS
20
D
THR
21
n
24
THR
21
D
GLN
22
n
25
GLN
22
D
ILE
23
n
26
ILE
23
D
LYS
24
n
27
LYS
24
D
ASN
25
n
28
ASN
25
D
GLY
26
n
29
GLY
26
D
GLU
27
n
30
GLU
27
D
LEU
28
n
31
LEU
28
D
GLN
29
n
32
GLN
29
D
PRO
30
n
33
PRO
30
D
ASP
31
n
34
ASP
31
D
MET
32
n
35
MET
32
D
PRO
33
n
36
PRO
33
D
LEU
34
n
37
LEU
34
D
PRO
35
n
38
PRO
35
D
SER
36
n
39
SER
36
D
GLU
37
n
40
GLU
37
D
ARG
38
n
41
ARG
38
D
GLU
39
n
42
GLU
39
D
TYR
40
n
43
TYR
40
D
ALA
41
n
44
ALA
41
D
GLU
42
n
45
GLU
42
D
GLN
43
n
46
GLN
43
D
PHE
44
n
47
PHE
44
D
GLY
45
n
48
GLY
45
D
ILE
46
n
49
ILE
46
D
SER
47
n
50
SER
47
D
ARG
48
n
51
ARG
48
D
MET
49
n
52
MET
49
D
THR
50
n
53
THR
50
D
VAL
51
n
54
VAL
51
D
ARG
52
n
55
ARG
52
D
GLN
53
n
56
GLN
53
D
ALA
54
n
57
ALA
54
D
LEU
55
n
58
LEU
55
D
SER
56
n
59
SER
56
D
ASN
57
n
60
ASN
57
D
LEU
58
n
61
LEU
58
D
VAL
59
n
62
VAL
59
D
ASN
60
n
63
ASN
60
D
GLU
61
n
64
GLU
61
D
GLY
62
n
65
GLY
62
D
LEU
63
n
66
LEU
63
D
LEU
64
n
67
LEU
64
D
TYR
65
n
68
TYR
65
D
ARG
66
n
69
ARG
66
D
LEU
67
n
70
LEU
67
D
LYS
68
n
71
LYS
68
D
GLY
69
n
72
GLY
69
D
ARG
70
n
73
ARG
70
D
GLY
71
n
74
GLY
71
D
THR
72
n
75
THR
72
D
PHE
73
n
76
PHE
73
D
VAL
74
n
77
VAL
74
D
SER
75
n
78
SER
75
D
DG
1
n
1
DG
1
E
DT
2
n
2
DT
2
E
DG
3
n
3
DG
3
E
DG
4
n
4
DG
4
E
DT
5
n
5
DT
5
E
DC
6
n
6
DC
6
E
DT
7
n
7
DT
7
E
DA
8
n
8
DA
8
E
DG
9
n
9
DG
9
E
DA
10
n
10
DA
10
E
DC
11
n
11
DC
11
E
DC
12
n
12
DC
12
E
DA
13
n
13
DA
13
E
DC
14
n
14
DC
14
E
DT
15
n
15
DT
15
E
DG
1
n
1
DG
1
F
DT
2
n
2
DT
2
F
DG
3
n
3
DG
3
F
DG
4
n
4
DG
4
F
DT
5
n
5
DT
5
F
DC
6
n
6
DC
6
F
DT
7
n
7
DT
7
F
DA
8
n
8
DA
8
F
DG
9
n
9
DG
9
F
DA
10
n
10
DA
10
F
DC
11
n
11
DC
11
F
DC
12
n
12
DC
12
F
DA
13
n
13
DA
13
F
DC
14
n
14
DC
14
F
DT
15
n
15
DT
15
F
author_and_software_defined_assembly
PISA
6
Hexameric
8830
-68
18350
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
TYR
65
A
N
TYR
68
A
O
PHE
73
A
O
PHE
76
B
N
TYR
65
B
N
TYR
68
B
O
PHE
73
B
O
PHE
76
C
N
TYR
65
C
N
TYR
68
C
O
PHE
73
C
O
PHE
76
D
N
TYR
65
D
N
TYR
68
D
O
PHE
73
D
O
PHE
76
1
A
GLY
-2
A
GLY
1
1
Y
1
A
SER
-1
A
SER
2
1
Y
1
A
HIS
0
A
HIS
3
1
Y
1
B
GLY
-2
B
GLY
1
1
Y
1
B
SER
-1
B
SER
2
1
Y
1
B
HIS
0
B
HIS
3
1
Y
1
C
GLY
-2
C
GLY
1
1
Y
1
C
SER
-1
C
SER
2
1
Y
1
C
HIS
0
C
HIS
3
1
Y
1
D
GLY
-2
D
GLY
1
1
Y
1
D
SER
-1
D
SER
2
1
Y
1
D
HIS
0
D
HIS
3
1
Y
1
D
MET
1
D
MET
4
1
Y
1
A
A
O
O
HOH
HOH
101
143
2.11
1
F
F
OP2
O
DA
HOH
8
101
2.13
1
E
F
O
O
HOH
HOH
143
140
2.16
1
B
B
O
O
MET
HOH
1
201
2.18
1
C
C
O
O
HOH
HOH
203
214
2.19
1
3.17
0.50
120.30
123.47
B
B
B
NE
CZ
NH1
ARG
ARG
ARG
48
48
48
N
1
-4.85
0.80
102.40
97.55
E
E
E
C3'
C2'
C1'
DG
DG
DG
1
1
1
N
1
4.27
0.30
108.30
112.57
E
E
E
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
2.35
0.30
108.30
110.65
E
E
E
O4'
C1'
N9
DA
DA
DA
8
8
8
N
1
4.71
0.30
108.30
113.01
F
F
F
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
2.07
0.30
108.30
110.37
F
F
F
O4'
C1'
N9
DA
DA
DA
8
8
8
N
1
A
ASP
31
55.15
19.53
1
A
PRO
35
-49.14
152.16
1
A
ARG
70
-122.43
-54.32
1
B
ARG
70
-124.01
-57.30
1
B
ARG
70
-123.55
-58.28
1
C
ASP
31
57.18
19.68
1
C
ARG
70
-134.92
-47.92
1
D
PRO
30
-39.65
132.75
1
D
ARG
70
-132.86
-49.20
99.380
29.8537
13.230
0.2294
0.1783
0.1809
1.91
32.52
1558
29632
31190
5.0000
99.6700
1.000
0.450
0.8245
0.2300
Random selection
1
FREE R-VALUE
1.950
MOLECULAR REPLACEMENT
25.1400
0.9000
1.1100
DNA-binding domain of PDB entry 2wv0
ML
FLAT BULK SOLVENT MODEL
1.91
32.52
287
3323
2
614
2420
0.007
3176
1.087
4407
0.046
482
0.005
472
19.676
1303
0.3129
0.2671
1.9758
139
2660
2799
11
98.0000
0.2900
0.2338
2.0464
143
2716
2859
11
100.0000
0.2585
0.2193
2.1283
140
2674
2814
11
100.0000
0.2877
0.2059
2.2252
143
2712
2855
11
100.0000
0.2816
0.2055
2.3425
141
2695
2836
11
100.0000
0.2341
0.1950
2.4892
142
2684
2826
11
100.0000
0.2387
0.1977
2.6813
144
2740
2884
11
100.0000
0.2567
0.1916
2.9510
140
2657
2797
11
100.0000
0.2488
0.1698
3.3776
142
2708
2850
11
100.0000
0.1951
0.1482
4.2539
141
2686
2827
11
100.0000
0.1788
0.1476
32.5286
143
2700
2843
11
100.0000
25.860
1.91
32.52
4U0Y
31230
0.085
1
10.61
3.8
99.8
0.87
1.91
1.98
1.90
1
3.7
98.7
data reduction
XDS
phasing
PHASER
refinement
PHENIX
(phenix.refine: 1.8.4_1496)
Crystal structure of the DNA-binding domains of YvoA in complex with palindromic operator DNA
1
N
N
1
N
N
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
4
N
N
4
N
N
4
N
N
4
N
N
4
N
N
4
N
N
A
PRO
10
A
PRO
13
HELX_P
A
ASN
25
A
ASN
28
1
AA1
16
A
SER
36
A
SER
39
HELX_P
A
GLY
45
A
GLY
48
1
AA2
10
A
SER
47
A
SER
50
HELX_P
A
GLU
61
A
GLU
64
1
AA3
15
B
PRO
10
B
PRO
13
HELX_P
B
GLY
26
B
GLY
29
1
AA4
17
B
SER
36
B
SER
39
HELX_P
B
GLY
45
B
GLY
48
1
AA5
10
B
SER
47
B
SER
50
HELX_P
B
GLU
61
B
GLU
64
1
AA6
15
C
PRO
10
C
PRO
13
HELX_P
C
ASN
25
C
ASN
28
1
AA7
16
C
SER
36
C
SER
39
HELX_P
C
GLY
45
C
GLY
48
1
AA8
10
C
SER
47
C
SER
50
HELX_P
C
GLU
61
C
GLU
64
1
AA9
15
D
PRO
10
D
PRO
13
HELX_P
D
ASN
25
D
ASN
28
1
AB1
16
D
SER
36
D
SER
39
HELX_P
D
GLY
45
D
GLY
48
1
AB2
10
D
SER
47
D
SER
50
HELX_P
D
GLU
61
D
GLU
64
1
AB3
15
hydrog
WATSON-CRICK
E
DG
1
E
N1
DG
1
1_555
F
DC
14
F
N3
DC
14
1_555
hydrog
WATSON-CRICK
E
DG
1
E
N2
DG
1
1_555
F
DC
14
F
O2
DC
14
1_555
hydrog
WATSON-CRICK
E
DG
1
E
O6
DG
1
1_555
F
DC
14
F
N4
DC
14
1_555
hydrog
WATSON-CRICK
E
DT
2
E
N3
DT
2
1_555
F
DA
13
F
N1
DA
13
1_555
hydrog
WATSON-CRICK
E
DT
2
E
O4
DT
2
1_555
F
DA
13
F
N6
DA
13
1_555
hydrog
WATSON-CRICK
E
DG
3
E
N1
DG
3
1_555
F
DC
12
F
N3
DC
12
1_555
hydrog
WATSON-CRICK
E
DG
3
E
N2
DG
3
1_555
F
DC
12
F
O2
DC
12
1_555
hydrog
WATSON-CRICK
E
DG
3
E
O6
DG
3
1_555
F
DC
12
F
N4
DC
12
1_555
hydrog
WATSON-CRICK
E
DG
4
E
N1
DG
4
1_555
F
DC
11
F
N3
DC
11
1_555
hydrog
WATSON-CRICK
E
DG
4
E
N2
DG
4
1_555
F
DC
11
F
O2
DC
11
1_555
hydrog
WATSON-CRICK
E
DG
4
E
O6
DG
4
1_555
F
DC
11
F
N4
DC
11
1_555
hydrog
WATSON-CRICK
E
DT
5
E
N3
DT
5
1_555
F
DA
10
F
N1
DA
10
1_555
hydrog
WATSON-CRICK
E
DT
5
E
O4
DT
5
1_555
F
DA
10
F
N6
DA
10
1_555
hydrog
WATSON-CRICK
E
DC
6
E
N3
DC
6
1_555
F
DG
9
F
N1
DG
9
1_555
hydrog
WATSON-CRICK
E
DC
6
E
N4
DC
6
1_555
F
DG
9
F
O6
DG
9
1_555
hydrog
WATSON-CRICK
E
DC
6
E
O2
DC
6
1_555
F
DG
9
F
N2
DG
9
1_555
hydrog
WATSON-CRICK
E
DT
7
E
N3
DT
7
1_555
F
DA
8
F
N1
DA
8
1_555
hydrog
WATSON-CRICK
E
DT
7
E
O4
DT
7
1_555
F
DA
8
F
N6
DA
8
1_555
hydrog
WATSON-CRICK
E
DA
8
E
N1
DA
8
1_555
F
DT
7
F
N3
DT
7
1_555
hydrog
WATSON-CRICK
E
DA
8
E
N6
DA
8
1_555
F
DT
7
F
O4
DT
7
1_555
hydrog
WATSON-CRICK
E
DG
9
E
N1
DG
9
1_555
F
DC
6
F
N3
DC
6
1_555
hydrog
WATSON-CRICK
E
DG
9
E
N2
DG
9
1_555
F
DC
6
F
O2
DC
6
1_555
hydrog
WATSON-CRICK
E
DG
9
E
O6
DG
9
1_555
F
DC
6
F
N4
DC
6
1_555
hydrog
WATSON-CRICK
E
DA
10
E
N1
DA
10
1_555
F
DT
5
F
N3
DT
5
1_555
hydrog
WATSON-CRICK
E
DA
10
E
N6
DA
10
1_555
F
DT
5
F
O4
DT
5
1_555
hydrog
WATSON-CRICK
E
DC
11
E
N3
DC
11
1_555
F
DG
4
F
N1
DG
4
1_555
hydrog
WATSON-CRICK
E
DC
11
E
N4
DC
11
1_555
F
DG
4
F
O6
DG
4
1_555
hydrog
WATSON-CRICK
E
DC
11
E
O2
DC
11
1_555
F
DG
4
F
N2
DG
4
1_555
hydrog
WATSON-CRICK
E
DC
12
E
N3
DC
12
1_555
F
DG
3
F
N1
DG
3
1_555
hydrog
WATSON-CRICK
E
DC
12
E
N4
DC
12
1_555
F
DG
3
F
O6
DG
3
1_555
hydrog
WATSON-CRICK
E
DC
12
E
O2
DC
12
1_555
F
DG
3
F
N2
DG
3
1_555
hydrog
WATSON-CRICK
E
DA
13
E
N1
DA
13
1_555
F
DT
2
F
N3
DT
2
1_555
hydrog
WATSON-CRICK
E
DA
13
E
N6
DA
13
1_555
F
DT
2
F
O4
DT
2
1_555
hydrog
WATSON-CRICK
E
DC
14
E
N3
DC
14
1_555
F
DG
1
F
N1
DG
1
1_555
hydrog
WATSON-CRICK
E
DC
14
E
N4
DC
14
1_555
F
DG
1
F
O6
DG
1
1_555
hydrog
WATSON-CRICK
E
DC
14
E
O2
DC
14
1_555
F
DG
1
F
N2
DG
1
1_555
TRANSCRIPTION
Transcription, Repressor, Bacterial transcription regulation, Transcription factor, GntR/HutC family, Winged helix-turn-helix motif, N-acetylglucosamine utilization, DNA-binding, Operator-binding
YVOA_BACSU
UNP
1
1
O34817
MNINKQSPIPIYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGRGTFVS
4U0Y
PDB
2
1
4U0Y
1
75
4U0Y
1
75
O34817
A
1
4
78
1
75
4U0Y
1
75
O34817
B
1
4
78
1
75
4U0Y
1
75
O34817
C
1
4
78
1
75
4U0Y
1
75
O34817
D
1
4
78
1
15
4U0Y
1
15
4U0Y
E
2
1
15
1
15
4U0Y
1
15
4U0Y
F
2
1
15
1
expression tag
GLY
-2
4U0Y
A
O34817
UNP
1
1
expression tag
SER
-1
4U0Y
A
O34817
UNP
2
1
expression tag
HIS
0
4U0Y
A
O34817
UNP
3
2
expression tag
GLY
-2
4U0Y
B
O34817
UNP
1
2
expression tag
SER
-1
4U0Y
B
O34817
UNP
2
2
expression tag
HIS
0
4U0Y
B
O34817
UNP
3
3
expression tag
GLY
-2
4U0Y
C
O34817
UNP
1
3
expression tag
SER
-1
4U0Y
C
O34817
UNP
2
3
expression tag
HIS
0
4U0Y
C
O34817
UNP
3
4
expression tag
GLY
-2
4U0Y
D
O34817
UNP
1
4
expression tag
SER
-1
4U0Y
D
O34817
UNP
2
4
expression tag
HIS
0
4U0Y
D
O34817
UNP
3
2
2
2
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LEU
64
A
LEU
67
A
LEU
67
A
LEU
70
A
GLY
71
A
GLY
74
A
VAL
74
A
VAL
77
B
LEU
64
B
LEU
67
B
LEU
67
B
LEU
70
B
GLY
71
B
GLY
74
B
VAL
74
B
VAL
77
C
LEU
64
C
LEU
67
C
LEU
67
C
LEU
70
C
GLY
71
C
GLY
74
C
VAL
74
C
VAL
77
D
LEU
64
D
LEU
67
D
LEU
67
D
LEU
70
D
GLY
71
D
GLY
74
D
VAL
74
D
VAL
77
binding site for residue CL B 101
B
CL
101
Software
4
binding site for residue CL C 101
C
CL
101
Software
4
A
ARG
48
A
ARG
51
4
1_555
B
ARG
38
B
ARG
41
4
1_555
E
DC
11
E
DC
11
4
1_555
E
HOH
131
M
HOH
4
1_555
C
ARG
48
C
ARG
51
4
1_555
D
ARG
38
D
ARG
41
4
1_555
F
DC
11
F
DC
11
4
1_555
F
HOH
129
N
HOH
4
1_555
144
P 31