0.013159
0.000000
0.004066
0.000000
0.023527
0.000000
0.000000
0.000000
0.010090
0.00000
0.00000
0.00000
Weihofen, W.A.
Cicek, A.
Pratto, F.
Alonso, J.C.
Saenger, W.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
107.17
90.00
75.991
42.505
103.727
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
C5 H9 N O2
115.130
y
PROLINE
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
N
384
N
C
N
385
N
C
N
386
N
O
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
N
N
397
S
C
N
398
N
C
N
399
N
O
N
400
R
C
N
401
N
O
N
402
N
C
N
403
N
O
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
N
N
414
S
C
N
415
N
C
N
416
N
O
N
417
N
C
Y
418
N
C
Y
419
N
C
Y
420
N
C
Y
421
N
C
Y
422
N
C
Y
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
H
N
434
N
H
N
435
N
H
N
436
N
H
N
437
N
N
N
438
S
C
N
439
N
C
N
440
N
O
N
441
N
C
N
442
N
C
N
443
N
C
N
444
N
O
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
H
N
452
N
H
N
453
N
H
N
454
N
H
N
455
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
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
doub
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
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
doub
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
Y
417
N
doub
Y
418
N
sing
Y
419
N
sing
N
420
N
sing
Y
421
N
doub
N
422
N
sing
Y
423
N
doub
N
424
N
sing
Y
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
sing
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
doub
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
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
34
1450
10.1093/NAR/GKL015
16528102
Structures of Omega Repressors Bound to Direct and Inverted DNA Repeats Explain Modulation of Transcription.
2006
10.2210/pdb2bnz/pdb
pdb_00002bnz
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
CCD
2004-10-15
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
1.08
1.0
14.1
BESSY
1.08
SYNCHROTRON
BESSY BEAMLINE 14.1
6137.223
ORF OMEGA
RIBBON-HELIX-HELIX DOMAIN, RESIDUES 20-71
4
man
polymer
SEQUENCE\: 5'- GAA TCA CAA GTG ATT AGC -3', 18MER DNA OLIGONUCLEOTIDE, FIRST STRAND, INVERTED DNA HEPTAD REPEATS (5'- AATCAC A/T -3'), NUCLEOTIDES G5 - G16, G18 AND E18 WERE NOT MODELLED
5548.630
5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*GP *TP*GP*AP*TP*TP*AP*GP*C)-3'
2
syn
polymer
SEQUENCE\: 5'- CTA ATC ACT TGT GAT TCG -3', 18MER DNA OLIGONUCLEOTIDE, SECOND STRAND, NUCLEOTIDES H19 - H31 WERE NOT MODELLED
5481.564
5'-D(*CP*TP*AP*AP*TP*CP*AP*CP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3'
2
syn
polymer
18.015
water
45
nat
water
OMEGA TRANSCRIPTIONAL REPRESSOR, ORF OMEGA'
no
no
MAKKDIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL
MAKKDIMGDKTVRVRADLHHIIKIETAKNGGNVKEVMDQALEEYIRKYLPDKL
A,B,C,D
polypeptide(L)
no
no
(DG)(DA)(DA)(DT)(DC)(DA)(DC)(DA)(DA)(DG)(DT)(DG)(DA)(DT)(DT)(DA)(DG)(DC)
GAATCACAAGTGATTAGC
E,G
polydeoxyribonucleotide
no
no
(DC)(DT)(DA)(DA)(DT)(DC)(DA)(DC)(DT)(DT)(DG)(DT)(DG)(DA)(DT)(DT)(DC)(DG)
CTAATCACTTGTGATTCG
F,H
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
sample
OMEGA TRANSCRIPTIONAL REPRESSOR IS ENCODED BY PLASMID PSM19035 OF THE INC18 FAMILY OF PLASMIDS
1314
STREPTOCOCCUS PYOGENES
511693
ESCHERICHIA COLI
BL21
PLASMID
PET28A-DELTA19OMEGA
1
3.6
65.9
7.50
120 MM NA/KPO4, PH 7.2, 2.2 M DINATRIUMMALONATE, PH 7.5, 3 % 2-METHYL-2,4-PENTANDIOL
1.288
1
19
F
19
E
17
2.927
F_DC19:DG17_E
1
-20.867
-1.125
0.551
0.355
10.300
1
20
F
20
E
16
8.255
F_DT20:DA16_E
2
-18.426
-0.166
-0.277
0.297
2.123
1
20
F
21
E
15
-0.833
F_DA21:DT15_E
3
-14.595
0.188
-0.163
-0.067
1.263
1
20
F
22
E
14
3.417
F_DA22:DT14_E
4
-9.074
0.068
0.316
-0.200
0.388
1
20
F
23
E
13
0.992
F_DT23:DA13_E
5
-8.466
-0.153
0.061
-0.210
-4.932
1
19
F
24
E
12
1.729
F_DC24:DG12_E
6
-16.059
0.266
-0.026
-0.206
4.607
1
20
F
25
E
11
1.397
F_DA25:DT11_E
7
2.074
0.083
-0.028
-0.135
5.022
1
19
F
26
E
10
-1.372
F_DC26:DG10_E
8
-7.016
0.065
0.119
-0.236
-6.912
1
20
F
27
E
9
-3.327
F_DT27:DA9_E
9
-13.240
-0.656
0.164
-0.393
-5.873
1
20
F
28
E
8
1.143
F_DT28:DA8_E
10
-10.408
0.031
0.076
-0.455
-18.870
1
19
F
29
E
7
0.605
F_DG29:DC7_E
11
-6.562
-0.118
-0.011
-0.316
-0.024
1
20
F
30
E
6
0.654
F_DT30:DA6_E
12
0.175
-0.191
-0.207
-0.291
8.706
1
19
F
31
E
5
1.150
F_DG31:DC5_E
13
-11.017
-0.320
0.270
-0.102
4.874
1
20
F
32
E
4
2.802
F_DA32:DT4_E
14
-14.553
-0.035
0.395
-0.206
1.808
1
20
F
33
E
3
1.470
F_DT33:DA3_E
15
-14.695
0.131
0.278
-0.150
-7.629
1
20
F
34
E
2
0.608
F_DT34:DA2_E
16
-12.218
-0.063
0.105
-0.181
15.429
1
19
F
35
E
1
0.468
F_DC35:DG1_E
17
-10.970
-0.320
-0.260
-0.200
-2.045
1
19
G
1
H
35
-1.435
G_DG1:DC35_H
18
-5.377
-1.444
-1.107
-0.486
4.963
1
20
G
2
H
34
-0.351
G_DA2:DT34_H
19
-12.300
-1.198
-0.479
0.305
11.774
1
G
3
H
33
15.471
G_DA3:DT33_H
20
-26.120
0.731
0.762
0.110
19.176
G
4
H
32
24.393
G_DT4:DA32_H
21
-40.601
-0.625
-1.043
0.374
3.410
37.331
F
F
19
20
-2.972
E
E
17
16
3.355
-1.890
0.622
-0.027
FF_DC19DT20:DA16DG17_EE
1
7.324
-11.517
36.584
0.218
0.039
3.571
45.751
F
F
20
21
0.847
E
E
16
15
3.571
0.659
-0.096
0.638
FF_DT20DA21:DT15DA16_EE
2
2.194
-2.823
45.697
0.758
0.332
3.086
35.377
F
F
21
22
-2.110
E
E
15
14
3.161
-1.278
0.474
-0.454
FF_DA21DA22:DT14DT15_EE
3
-4.794
7.913
35.038
-0.566
-1.458
3.401
30.695
F
F
22
23
-9.332
E
E
14
13
3.327
-4.917
-0.250
-0.871
FF_DA22DT23:DA13DT14_EE
4
1.867
-3.544
30.252
-0.643
0.852
3.290
42.316
F
F
23
24
-9.361
E
E
13
12
3.294
-6.728
-0.031
-0.273
FF_DT23DC24:DG12DA13_EE
5
2.513
-3.496
41.730
0.319
0.304
3.182
39.122
F
F
24
25
-8.728
E
E
12
11
3.382
-5.824
1.040
1.328
FF_DC24DA25:DT11DG12_EE
6
0.993
-1.488
38.691
2.689
-1.433
3.346
31.555
F
F
25
26
1.318
E
E
11
10
3.282
0.716
-0.900
-0.251
FF_DA25DC26:DG10DT11_EE
7
-3.084
5.680
31.400
-0.596
1.073
3.441
35.736
F
F
26
27
-1.618
E
E
10
9
3.408
-0.993
-0.037
-1.419
FF_DC26DT27:DA9DG10_EE
8
1.378
-2.246
35.697
-2.162
0.268
3.310
40.877
F
F
27
28
-5.795
E
E
9
8
3.291
-4.041
0.216
-0.343
FF_DT27DT28:DA8DA9_EE
9
0.278
-0.398
40.685
-0.042
-0.279
3.563
40.328
F
F
28
29
-0.425
E
E
8
7
3.570
-0.293
0.169
-0.218
FF_DT28DG29:DC7DA8_EE
10
-1.536
2.229
40.299
-0.281
-0.433
2.962
23.815
F
F
29
30
-3.407
E
E
7
6
2.981
-1.403
-0.068
-0.081
FF_DG29DT30:DA6DC7_EE
11
2.150
-5.219
23.678
0.223
0.808
2.939
43.289
F
F
30
31
-14.768
E
E
6
5
3.461
-10.789
-0.314
1.798
FF_DT30DG31:DC5DA6_EE
12
-0.925
1.266
41.976
3.485
0.336
3.360
38.614
F
F
31
32
-2.505
E
E
5
4
3.353
-1.656
0.437
-0.199
FF_DG31DA32:DT4DC5_EE
13
0.175
-0.265
38.579
-0.091
-0.639
3.505
33.359
F
F
32
33
-7.871
E
E
4
3
3.397
-4.505
0.332
-0.993
FF_DA32DT33:DA3DT4_EE
14
0.779
-1.362
33.053
-0.937
-0.442
3.363
34.764
F
F
33
34
0.875
E
E
3
2
3.388
0.522
-0.047
-0.653
FF_DT33DT34:DA2DA3_EE
15
2.969
-4.976
34.637
-1.175
0.547
2.766
33.741
F
F
34
35
1.942
E
E
2
1
2.776
1.127
0.332
-0.061
FF_DT34DC35:DG1DA2_EE
16
-0.627
1.081
33.717
-0.259
-0.659
4.006
-121.723
F
G
35
1
9.476
E
H
1
35
4.441
-16.534
-0.020
-5.186
FG_DC35DG1:DC35DG1_HE
17
2.824
1.618
-121.031
3.165
0.022
3.085
37.892
G
G
1
2
17.124
H
H
35
34
3.055
10.885
-0.486
0.429
GG_DG1DA2:DT34DC35_HH
18
-8.347
13.132
35.407
-0.696
-0.293
2.876
51.171
G
G
2
3
-2.858
H
H
34
33
2.931
-2.467
0.476
0.566
GG_DA2DA3:DT33DT34_HH
19
-2.660
3.081
51.051
0.806
-0.714
2.472
29.505
G
G
3
4
-0.056
H
H
33
32
2.896
-0.028
-0.267
0.025
GG_DA3DT4:DA32DT33_HH
20
13.417
-27.306
26.339
0.054
3.009
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_status
pdbx_initial_refinement_model
repository
Initial release
Advisory
Version format compliance
Other
Source and taxonomy
Data collection
Database references
Other
Refinement description
1
0
2006-03-15
1
1
2011-07-13
1
2
2015-10-21
1
3
2023-12-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_sf
CRYSTAL STRUCTURE OF OMEGA TRANSCRIPTIONAL REPRESSOR AT1.5A RESOLUTION
STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX OMEGA REPRESSOR TO DIRECT DNA HEPTAD REPEATS
STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX REPRESSOR OMEGA TO MUTATED DIRECT DNA HEPTAD REPEATS
PDBE
Y
PDBE
2005-04-06
REL
REL
HOH
water
INVERTED REPEATS OCCUR IN PROMOTER REGIONS PRECEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL REPRESSOR, PLASMID PSM19035
32630
SYNTHETIC CONSTRUCT
sample
INVERTED REPEATS OCCUR IN PROMOTER REGIONS PRECEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL REPRESSOR, PLASMID PSM19035
32630
SYNTHETIC CONSTRUCT
sample
19 N-TERMINAL RESIDUES TRUNCATED, NEW N-TERMINAL MET19 IS
A CLONING ARTEFACT
2BNW
PDB ENTRY 2BNW
PDB
experimental model
HOH
2001
4
HOH
HOH
2001
A
HOH
2002
4
HOH
HOH
2002
A
HOH
2003
4
HOH
HOH
2003
A
HOH
2001
4
HOH
HOH
2001
B
HOH
2002
4
HOH
HOH
2002
B
HOH
2003
4
HOH
HOH
2003
B
HOH
2004
4
HOH
HOH
2004
B
HOH
2005
4
HOH
HOH
2005
B
HOH
2006
4
HOH
HOH
2006
B
HOH
2007
4
HOH
HOH
2007
B
HOH
2008
4
HOH
HOH
2008
B
HOH
2009
4
HOH
HOH
2009
B
HOH
2010
4
HOH
HOH
2010
B
HOH
2001
4
HOH
HOH
2001
C
HOH
2002
4
HOH
HOH
2002
C
HOH
2003
4
HOH
HOH
2003
C
HOH
2004
4
HOH
HOH
2004
C
HOH
2005
4
HOH
HOH
2005
C
HOH
2006
4
HOH
HOH
2006
C
HOH
2007
4
HOH
HOH
2007
C
HOH
2008
4
HOH
HOH
2008
C
HOH
2009
4
HOH
HOH
2009
C
HOH
2001
4
HOH
HOH
2001
D
HOH
2002
4
HOH
HOH
2002
D
HOH
2003
4
HOH
HOH
2003
D
HOH
2001
4
HOH
HOH
2001
E
HOH
2002
4
HOH
HOH
2002
E
HOH
2003
4
HOH
HOH
2003
E
HOH
2004
4
HOH
HOH
2004
E
HOH
2005
4
HOH
HOH
2005
E
HOH
2006
4
HOH
HOH
2006
E
HOH
2007
4
HOH
HOH
2007
E
HOH
2008
4
HOH
HOH
2008
E
HOH
2009
4
HOH
HOH
2009
E
HOH
2001
4
HOH
HOH
2001
F
HOH
2002
4
HOH
HOH
2002
F
HOH
2003
4
HOH
HOH
2003
F
HOH
2004
4
HOH
HOH
2004
F
HOH
2005
4
HOH
HOH
2005
F
HOH
2006
4
HOH
HOH
2006
F
HOH
2007
4
HOH
HOH
2007
F
HOH
2008
4
HOH
HOH
2008
F
HOH
2009
4
HOH
HOH
2009
F
HOH
2010
4
HOH
HOH
2010
F
HOH
2001
4
HOH
HOH
2001
H
n
1
19
A
n
2
20
A
n
3
21
A
LYS
22
n
4
LYS
22
A
ASP
23
n
5
ASP
23
A
ILE
24
n
6
ILE
24
A
MET
25
n
7
MET
25
A
GLY
26
n
8
GLY
26
A
ASP
27
n
9
ASP
27
A
LYS
28
n
10
LYS
28
A
THR
29
n
11
THR
29
A
VAL
30
n
12
VAL
30
A
ARG
31
n
13
ARG
31
A
VAL
32
n
14
VAL
32
A
ARG
33
n
15
ARG
33
A
ALA
34
n
16
ALA
34
A
ASP
35
n
17
ASP
35
A
LEU
36
n
18
LEU
36
A
HIS
37
n
19
HIS
37
A
HIS
38
n
20
HIS
38
A
ILE
39
n
21
ILE
39
A
ILE
40
n
22
ILE
40
A
LYS
41
n
23
LYS
41
A
ILE
42
n
24
ILE
42
A
GLU
43
n
25
GLU
43
A
THR
44
n
26
THR
44
A
ALA
45
n
27
ALA
45
A
LYS
46
n
28
LYS
46
A
ASN
47
n
29
ASN
47
A
GLY
48
n
30
GLY
48
A
GLY
49
n
31
GLY
49
A
ASN
50
n
32
ASN
50
A
VAL
51
n
33
VAL
51
A
LYS
52
n
34
LYS
52
A
GLU
53
n
35
GLU
53
A
VAL
54
n
36
VAL
54
A
MET
55
n
37
MET
55
A
ASP
56
n
38
ASP
56
A
GLN
57
n
39
GLN
57
A
ALA
58
n
40
ALA
58
A
LEU
59
n
41
LEU
59
A
GLU
60
n
42
GLU
60
A
GLU
61
n
43
GLU
61
A
TYR
62
n
44
TYR
62
A
ILE
63
n
45
ILE
63
A
ARG
64
n
46
ARG
64
A
LYS
65
n
47
LYS
65
A
TYR
66
n
48
TYR
66
A
LEU
67
n
49
LEU
67
A
PRO
68
n
50
PRO
68
A
ASP
69
n
51
ASP
69
A
LYS
70
n
52
LYS
70
A
LEU
71
n
53
LEU
71
A
n
1
19
B
n
2
20
B
n
3
21
B
LYS
22
n
4
LYS
22
B
ASP
23
n
5
ASP
23
B
ILE
24
n
6
ILE
24
B
MET
25
n
7
MET
25
B
GLY
26
n
8
GLY
26
B
ASP
27
n
9
ASP
27
B
LYS
28
n
10
LYS
28
B
THR
29
n
11
THR
29
B
VAL
30
n
12
VAL
30
B
ARG
31
n
13
ARG
31
B
VAL
32
n
14
VAL
32
B
ARG
33
n
15
ARG
33
B
ALA
34
n
16
ALA
34
B
ASP
35
n
17
ASP
35
B
LEU
36
n
18
LEU
36
B
HIS
37
n
19
HIS
37
B
HIS
38
n
20
HIS
38
B
ILE
39
n
21
ILE
39
B
ILE
40
n
22
ILE
40
B
LYS
41
n
23
LYS
41
B
ILE
42
n
24
ILE
42
B
GLU
43
n
25
GLU
43
B
THR
44
n
26
THR
44
B
ALA
45
n
27
ALA
45
B
LYS
46
n
28
LYS
46
B
ASN
47
n
29
ASN
47
B
GLY
48
n
30
GLY
48
B
GLY
49
n
31
GLY
49
B
ASN
50
n
32
ASN
50
B
VAL
51
n
33
VAL
51
B
LYS
52
n
34
LYS
52
B
GLU
53
n
35
GLU
53
B
VAL
54
n
36
VAL
54
B
MET
55
n
37
MET
55
B
ASP
56
n
38
ASP
56
B
GLN
57
n
39
GLN
57
B
ALA
58
n
40
ALA
58
B
LEU
59
n
41
LEU
59
B
GLU
60
n
42
GLU
60
B
GLU
61
n
43
GLU
61
B
TYR
62
n
44
TYR
62
B
ILE
63
n
45
ILE
63
B
ARG
64
n
46
ARG
64
B
LYS
65
n
47
LYS
65
B
TYR
66
n
48
TYR
66
B
LEU
67
n
49
LEU
67
B
PRO
68
n
50
PRO
68
B
ASP
69
n
51
ASP
69
B
LYS
70
n
52
LYS
70
B
LEU
71
n
53
LEU
71
B
n
1
19
C
ALA
20
n
2
ALA
20
C
LYS
21
n
3
LYS
21
C
LYS
22
n
4
LYS
22
C
ASP
23
n
5
ASP
23
C
ILE
24
n
6
ILE
24
C
MET
25
n
7
MET
25
C
GLY
26
n
8
GLY
26
C
ASP
27
n
9
ASP
27
C
LYS
28
n
10
LYS
28
C
THR
29
n
11
THR
29
C
VAL
30
n
12
VAL
30
C
ARG
31
n
13
ARG
31
C
VAL
32
n
14
VAL
32
C
ARG
33
n
15
ARG
33
C
ALA
34
n
16
ALA
34
C
ASP
35
n
17
ASP
35
C
LEU
36
n
18
LEU
36
C
HIS
37
n
19
HIS
37
C
HIS
38
n
20
HIS
38
C
ILE
39
n
21
ILE
39
C
ILE
40
n
22
ILE
40
C
LYS
41
n
23
LYS
41
C
ILE
42
n
24
ILE
42
C
GLU
43
n
25
GLU
43
C
THR
44
n
26
THR
44
C
ALA
45
n
27
ALA
45
C
LYS
46
n
28
LYS
46
C
ASN
47
n
29
ASN
47
C
GLY
48
n
30
GLY
48
C
GLY
49
n
31
GLY
49
C
ASN
50
n
32
ASN
50
C
VAL
51
n
33
VAL
51
C
LYS
52
n
34
LYS
52
C
GLU
53
n
35
GLU
53
C
VAL
54
n
36
VAL
54
C
MET
55
n
37
MET
55
C
ASP
56
n
38
ASP
56
C
GLN
57
n
39
GLN
57
C
ALA
58
n
40
ALA
58
C
LEU
59
n
41
LEU
59
C
GLU
60
n
42
GLU
60
C
GLU
61
n
43
GLU
61
C
TYR
62
n
44
TYR
62
C
ILE
63
n
45
ILE
63
C
ARG
64
n
46
ARG
64
C
LYS
65
n
47
LYS
65
C
TYR
66
n
48
TYR
66
C
LEU
67
n
49
LEU
67
C
PRO
68
n
50
PRO
68
C
ASP
69
n
51
ASP
69
C
LYS
70
n
52
LYS
70
C
LEU
71
n
53
LEU
71
C
n
1
19
D
n
2
20
D
n
3
21
D
n
4
22
D
n
5
23
D
n
6
24
D
MET
25
n
7
MET
25
D
GLY
26
n
8
GLY
26
D
ASP
27
n
9
ASP
27
D
LYS
28
n
10
LYS
28
D
THR
29
n
11
THR
29
D
VAL
30
n
12
VAL
30
D
ARG
31
n
13
ARG
31
D
VAL
32
n
14
VAL
32
D
ARG
33
n
15
ARG
33
D
ALA
34
n
16
ALA
34
D
ASP
35
n
17
ASP
35
D
LEU
36
n
18
LEU
36
D
HIS
37
n
19
HIS
37
D
HIS
38
n
20
HIS
38
D
ILE
39
n
21
ILE
39
D
ILE
40
n
22
ILE
40
D
LYS
41
n
23
LYS
41
D
ILE
42
n
24
ILE
42
D
GLU
43
n
25
GLU
43
D
THR
44
n
26
THR
44
D
ALA
45
n
27
ALA
45
D
LYS
46
n
28
LYS
46
D
ASN
47
n
29
ASN
47
D
GLY
48
n
30
GLY
48
D
GLY
49
n
31
GLY
49
D
ASN
50
n
32
ASN
50
D
VAL
51
n
33
VAL
51
D
LYS
52
n
34
LYS
52
D
GLU
53
n
35
GLU
53
D
VAL
54
n
36
VAL
54
D
MET
55
n
37
MET
55
D
ASP
56
n
38
ASP
56
D
GLN
57
n
39
GLN
57
D
ALA
58
n
40
ALA
58
D
LEU
59
n
41
LEU
59
D
GLU
60
n
42
GLU
60
D
GLU
61
n
43
GLU
61
D
TYR
62
n
44
TYR
62
D
ILE
63
n
45
ILE
63
D
ARG
64
n
46
ARG
64
D
LYS
65
n
47
LYS
65
D
TYR
66
n
48
TYR
66
D
LEU
67
n
49
LEU
67
D
PRO
68
n
50
PRO
68
D
ASP
69
n
51
ASP
69
D
LYS
70
n
52
LYS
70
D
LEU
71
n
53
LEU
71
D
DG
1
n
1
DG
1
E
DA
2
n
2
DA
2
E
DA
3
n
3
DA
3
E
DT
4
n
4
DT
4
E
DC
5
n
5
DC
5
E
DA
6
n
6
DA
6
E
DC
7
n
7
DC
7
E
DA
8
n
8
DA
8
E
DA
9
n
9
DA
9
E
DG
10
n
10
DG
10
E
DT
11
n
11
DT
11
E
DG
12
n
12
DG
12
E
DA
13
n
13
DA
13
E
DT
14
n
14
DT
14
E
DT
15
n
15
DT
15
E
DA
16
n
16
DA
16
E
DG
17
n
17
DG
17
E
n
18
18
E
DC
19
n
1
DC
19
F
DT
20
n
2
DT
20
F
DA
21
n
3
DA
21
F
DA
22
n
4
DA
22
F
DT
23
n
5
DT
23
F
DC
24
n
6
DC
24
F
DA
25
n
7
DA
25
F
DC
26
n
8
DC
26
F
DT
27
n
9
DT
27
F
DT
28
n
10
DT
28
F
DG
29
n
11
DG
29
F
DT
30
n
12
DT
30
F
DG
31
n
13
DG
31
F
DA
32
n
14
DA
32
F
DT
33
n
15
DT
33
F
DT
34
n
16
DT
34
F
DC
35
n
17
DC
35
F
DG
36
n
18
DG
36
F
DG
1
n
1
DG
1
G
DA
2
n
2
DA
2
G
DA
3
n
3
DA
3
G
DT
4
n
4
DT
4
G
n
5
12
G
n
6
13
G
n
7
14
G
n
8
15
G
n
9
16
G
DG
17
n
10
DG
17
G
n
11
18
G
n
12
19
G
n
13
20
G
n
14
21
G
n
15
22
G
n
16
23
G
n
17
24
G
n
18
25
G
n
1
19
H
n
2
20
H
n
3
21
H
n
4
22
H
n
5
23
H
n
6
24
H
n
7
25
H
n
8
26
H
n
9
27
H
n
10
28
H
n
11
29
H
n
12
30
H
n
13
31
H
DA
32
n
14
DA
32
H
DT
33
n
15
DT
33
H
DT
34
n
16
DT
34
H
DC
35
n
17
DC
35
H
DG
36
n
18
DG
36
H
2.4214
0.0862
-0.4518
0.8484
0.3186
1.1087
-0.1025
-0.0442
-0.0570
-0.0003
0.0593
0.0127
0.0301
0.0366
0.0431
-0.0533
-0.0011
-0.0088
-0.0834
0.0317
0.0287
refined
-11.7706
-13.0601
-2.2275
X-RAY DIFFRACTION
1.4921
-0.1307
-0.4571
1.7929
-0.8153
0.5507
-0.1373
-0.1088
-0.1180
-0.0515
0.1765
-0.0885
0.2074
-0.0539
-0.0392
-0.0425
0.0294
0.0334
-0.0456
0.0129
0.0116
refined
-9.4437
-19.7056
0.8256
X-RAY DIFFRACTION
1.7414
-0.9244
0.0054
3.1371
0.6820
1.1969
-0.1447
-0.2663
-0.0144
0.1131
0.0843
0.0168
0.0171
0.0876
0.0604
-0.0835
0.0402
-0.0122
-0.0381
-0.0223
-0.0227
refined
-32.7993
2.2285
12.2330
X-RAY DIFFRACTION
4.7769
0.0582
0.0258
4.2141
2.6243
2.3797
-0.0378
-0.1026
0.0817
0.0936
0.0820
0.0793
0.1904
-0.0060
-0.0442
-0.0928
0.0232
0.0193
-0.0759
0.0192
-0.0561
refined
-40.1214
-0.0091
11.7257
X-RAY DIFFRACTION
1.6400
-1.3528
-2.2065
1.1384
1.6186
4.7785
-0.0111
-0.1178
0.0360
-0.0067
0.0572
-0.1418
-0.1179
0.0202
-0.0460
-0.1130
-0.0104
-0.0163
-0.0335
-0.0138
-0.0268
refined
-17.5503
1.9413
4.6985
X-RAY DIFFRACTION
2.1353
-0.6071
-1.4997
1.4735
1.6292
4.3810
-0.0236
-0.1379
0.0798
-0.0230
0.0852
-0.1519
-0.0767
0.1700
-0.0616
-0.0929
0.0023
-0.0114
-0.1197
0.0117
-0.0379
refined
-18.9119
2.2400
4.0972
X-RAY DIFFRACTION
3.4902
-1.0287
-4.2756
1.2736
0.3236
6.1415
0.2926
0.2465
0.3769
-0.4101
0.0470
-0.2294
-0.1466
0.1533
-0.3396
0.2096
-0.0690
0.0574
0.2299
0.0640
-0.1959
refined
-8.0201
-8.1992
-19.3437
X-RAY DIFFRACTION
A
24
A
50
X-RAY DIFFRACTION
1
B
24
B
50
X-RAY DIFFRACTION
1
A
51
A
67
X-RAY DIFFRACTION
2
B
51
B
67
X-RAY DIFFRACTION
2
C
24
C
50
X-RAY DIFFRACTION
3
D
24
D
50
X-RAY DIFFRACTION
3
C
51
C
67
X-RAY DIFFRACTION
4
D
51
D
67
X-RAY DIFFRACTION
4
E
1
E
17
X-RAY DIFFRACTION
5
F
21
F
36
X-RAY DIFFRACTION
6
G
2
G
17
X-RAY DIFFRACTION
7
H
34
H
38
X-RAY DIFFRACTION
7
author_and_software_defined_assembly
PISA
8
octameric
12840
-104.2
15160
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
VAL
32
A
N
VAL
14
B
O
LYS
28
B
O
LYS
10
C
N
VAL
32
C
N
VAL
14
D
O
LYS
28
D
O
LYS
10
1
A
MET
19
A
MET
1
1
Y
1
A
ALA
20
A
ALA
2
1
Y
1
A
LYS
21
A
LYS
3
1
Y
1
B
MET
19
B
MET
1
1
Y
1
B
ALA
20
B
ALA
2
1
Y
1
B
LYS
21
B
LYS
3
1
Y
1
C
MET
19
C
MET
1
1
Y
1
D
MET
19
D
MET
1
1
Y
1
D
ALA
20
D
ALA
2
1
Y
1
D
LYS
21
D
LYS
3
1
Y
1
D
LYS
22
D
LYS
4
1
Y
1
D
ASP
23
D
ASP
5
1
Y
1
D
ILE
24
D
ILE
6
1
Y
1
E
DC
18
E
DC
18
1
Y
1
G
DC
12
G
DC
5
1
Y
1
G
DA
13
G
DA
6
1
Y
1
G
DC
14
G
DC
7
1
Y
1
G
DA
15
G
DA
8
1
Y
1
G
DA
16
G
DA
9
1
Y
1
G
DT
18
G
DT
11
1
Y
1
G
DG
19
G
DG
12
1
Y
1
G
DA
20
G
DA
13
1
Y
1
G
DT
21
G
DT
14
1
Y
1
G
DT
22
G
DT
15
1
Y
1
G
DA
23
G
DA
16
1
Y
1
G
DG
24
G
DG
17
1
Y
1
G
DC
25
G
DC
18
1
Y
1
H
DC
19
H
DC
1
1
Y
1
H
DT
20
H
DT
2
1
Y
1
H
DA
21
H
DA
3
1
Y
1
H
DA
22
H
DA
4
1
Y
1
H
DT
23
H
DT
5
1
Y
1
H
DC
24
H
DC
6
1
Y
1
H
DA
25
H
DA
7
1
Y
1
H
DC
26
H
DC
8
1
Y
1
H
DT
27
H
DT
9
1
Y
1
H
DT
28
H
DT
10
1
Y
1
H
DG
29
H
DG
11
1
Y
1
H
DT
30
H
DT
12
1
Y
1
H
DG
31
H
DG
13
1
Y
1
5.61
0.90
118.30
123.91
A
A
A
CB
CG
OD2
ASP
ASP
ASP
23
23
23
N
1
5.46
0.90
118.30
123.76
B
B
B
CB
CG
OD2
ASP
ASP
ASP
69
69
69
N
1
1.84
0.30
108.30
110.14
F
F
F
O4'
C1'
N1
DC
DC
DC
19
19
19
N
1
2.25
0.30
108.30
110.55
F
F
F
O4'
C1'
N1
DT
DT
DT
20
20
20
N
1
3.21
0.30
108.30
111.51
F
F
F
O4'
C1'
N1
DT
DT
DT
30
30
30
N
1
2.70
0.30
108.30
111.00
F
F
F
O4'
C1'
N9
DG
DG
DG
36
36
36
N
1
3.71
0.30
108.30
112.01
G
G
G
O4'
C1'
N9
DG
DG
DG
1
1
1
N
1
1.83
0.30
108.30
110.13
G
G
G
O4'
C1'
N9
DG
DG
DG
17
17
17
N
1
2.81
0.30
108.30
111.11
H
H
H
O4'
C1'
N1
DT
DT
DT
33
33
33
N
1
1.85
0.30
108.30
110.15
H
H
H
O4'
C1'
N1
DT
DT
DT
34
34
34
N
1
2.62
0.30
108.30
110.92
H
H
H
O4'
C1'
N1
DC
DC
DC
35
35
35
N
1
A
MET
25
157.06
118.33
1
B
ARG
33
-23.68
121.20
1
B
ASN
47
-106.35
-134.86
1
B
LEU
67
-141.03
50.12
34.17
-1.18000
0.00000
2.27000
0.10000
0.00000
2.42000
0.909
0.877
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NUCLEOTIDES G5-G16, G18, E18 AND H19-H31 WERE NOT MODELLED DUE TO PATCHY ELECTRON DENSITY
0.258
0.225
0.227
2.60
100.00
944
17564
5.100
92.8
18.753
0.202
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.365
0.268
0.80
0.80
1.20
PDB ENTRY 2BNW
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
2.60
100.00
45
2585
0
927
1613
0.012
0.021
2665
0.002
0.020
2009
1.044
2.410
3765
0.727
3.000
4771
6.435
5.000
195
33.312
24.667
75
17.026
15.000
349
18.490
15.000
12
0.051
0.200
426
0.006
0.020
2208
0.001
0.020
287
0.208
0.300
616
0.200
0.300
2265
0.206
0.500
1179
0.088
0.500
1301
0.209
0.400
164
0.110
0.300
10
0.181
0.300
46
0.217
0.400
8
0.878
2.000
1294
1.051
3.000
1594
0.554
2.000
2201
1.035
3.000
2171
0.4040
0.3660
2.67
48
981
20
2.600
35.000
2BNZ
18516
1.000
0.11000
1
11.7000
2.500
92.8
0.29000
2.60
2.69
3.100
1
1.90
72.2
refinement
REFMAC
5.2.0003
data reduction
DENZO
data scaling
SCALEPACK
phasing
MOLREP
Structural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to inverted DNA heptad repeats
1
N
N
1
N
N
1
N
N
1
N
N
2
N
N
3
N
N
2
N
N
3
N
N
4
N
N
4
N
N
4
N
N
4
N
N
4
N
N
4
N
N
4
N
N
THE DESIGNATION OF THE QUATERNARY STRUCTURE
AS OCTAMERICREFLECTS THE STANDARD PQS CONVENTION FOR
DESCRIBINGHETEROGENEOUS ASSEMBLIES. HOWEVER, THE
CRYSTALLOGRAPHICASYMMETRIC UNIT ACTUALLY CONTAINS ONE
DNA FRAGMENT(COMPRISED OF CHAINS E AND F) WHICH
IS BOUND TO TWOPROTEIN DIMERS (CHAINS A, B, C
AND D). A FURTHER FREEDNA FRAGMENT (CHAINS G
AND H) IS PRESENT IN THE A.U. BUTIS LARGELY
UNOBSERVED IN ELECTRON DENSITY MAPS.
A
ALA
34
A
ALA
16
HELX_P
A
ASN
47
A
ASN
29
1
1
14
A
ASN
50
A
ASN
32
HELX_P
A
LEU
67
A
LEU
49
1
2
18
A
PRO
68
A
PRO
50
HELX_P
A
LEU
71
A
LEU
53
5
3
4
B
ALA
34
B
ALA
16
HELX_P
B
ASN
47
B
ASN
29
1
4
14
B
ASN
50
B
ASN
32
HELX_P
B
LEU
67
B
LEU
49
1
5
18
B
PRO
68
B
PRO
50
HELX_P
B
LEU
71
B
LEU
53
5
6
4
C
ALA
20
C
ALA
2
HELX_P
C
MET
25
C
MET
7
1
7
6
C
ALA
34
C
ALA
16
HELX_P
C
ASN
47
C
ASN
29
1
8
14
C
ASN
50
C
ASN
32
HELX_P
C
LEU
67
C
LEU
49
1
9
18
C
PRO
68
C
PRO
50
HELX_P
C
LEU
71
C
LEU
53
5
10
4
D
ALA
34
D
ALA
16
HELX_P
D
ASN
47
D
ASN
29
1
11
14
D
ASN
50
D
ASN
32
HELX_P
D
LEU
67
D
LEU
49
1
12
18
hydrog
WATSON-CRICK
E
DG
1
E
N1
DG
1
1_555
F
DC
35
F
N3
DC
17
1_555
hydrog
WATSON-CRICK
E
DG
1
E
N2
DG
1
1_555
F
DC
35
F
O2
DC
17
1_555
hydrog
WATSON-CRICK
E
DG
1
E
O6
DG
1
1_555
F
DC
35
F
N4
DC
17
1_555
hydrog
TYPE_4_PAIR
E
DG
1
E
N2
DG
1
1_555
H
DG
36
H
N3
DG
18
1_555
hydrog
TYPE_4_PAIR
E
DG
1
E
N3
DG
1
1_555
H
DG
36
H
N2
DG
18
1_555
hydrog
WATSON-CRICK
E
DA
2
E
N1
DA
2
1_555
F
DT
34
F
N3
DT
16
1_555
hydrog
WATSON-CRICK
E
DA
2
E
N6
DA
2
1_555
F
DT
34
F
O4
DT
16
1_555
hydrog
WATSON-CRICK
E
DA
3
E
N1
DA
3
1_555
F
DT
33
F
N3
DT
15
1_555
hydrog
WATSON-CRICK
E
DA
3
E
N6
DA
3
1_555
F
DT
33
F
O4
DT
15
1_555
hydrog
WATSON-CRICK
E
DT
4
E
N3
DT
4
1_555
F
DA
32
F
N1
DA
14
1_555
hydrog
WATSON-CRICK
E
DT
4
E
O4
DT
4
1_555
F
DA
32
F
N6
DA
14
1_555
hydrog
WATSON-CRICK
E
DC
5
E
N3
DC
5
1_555
F
DG
31
F
N1
DG
13
1_555
hydrog
WATSON-CRICK
E
DC
5
E
N4
DC
5
1_555
F
DG
31
F
O6
DG
13
1_555
hydrog
WATSON-CRICK
E
DC
5
E
O2
DC
5
1_555
F
DG
31
F
N2
DG
13
1_555
hydrog
WATSON-CRICK
E
DA
6
E
N1
DA
6
1_555
F
DT
30
F
N3
DT
12
1_555
hydrog
WATSON-CRICK
E
DA
6
E
N6
DA
6
1_555
F
DT
30
F
O4
DT
12
1_555
hydrog
WATSON-CRICK
E
DC
7
E
N3
DC
7
1_555
F
DG
29
F
N1
DG
11
1_555
hydrog
WATSON-CRICK
E
DC
7
E
N4
DC
7
1_555
F
DG
29
F
O6
DG
11
1_555
hydrog
WATSON-CRICK
E
DC
7
E
O2
DC
7
1_555
F
DG
29
F
N2
DG
11
1_555
hydrog
WATSON-CRICK
E
DA
8
E
N1
DA
8
1_555
F
DT
28
F
N3
DT
10
1_555
hydrog
WATSON-CRICK
E
DA
8
E
N6
DA
8
1_555
F
DT
28
F
O4
DT
10
1_555
hydrog
WATSON-CRICK
E
DA
9
E
N1
DA
9
1_555
F
DT
27
F
N3
DT
9
1_555
hydrog
WATSON-CRICK
E
DA
9
E
N6
DA
9
1_555
F
DT
27
F
O4
DT
9
1_555
hydrog
WATSON-CRICK
E
DG
10
E
N1
DG
10
1_555
F
DC
26
F
N3
DC
8
1_555
hydrog
WATSON-CRICK
E
DG
10
E
N2
DG
10
1_555
F
DC
26
F
O2
DC
8
1_555
hydrog
WATSON-CRICK
E
DG
10
E
O6
DG
10
1_555
F
DC
26
F
N4
DC
8
1_555
hydrog
WATSON-CRICK
E
DT
11
E
N3
DT
11
1_555
F
DA
25
F
N1
DA
7
1_555
hydrog
WATSON-CRICK
E
DT
11
E
O4
DT
11
1_555
F
DA
25
F
N6
DA
7
1_555
hydrog
WATSON-CRICK
E
DG
12
E
N1
DG
12
1_555
F
DC
24
F
N3
DC
6
1_555
hydrog
WATSON-CRICK
E
DG
12
E
N2
DG
12
1_555
F
DC
24
F
O2
DC
6
1_555
hydrog
WATSON-CRICK
E
DG
12
E
O6
DG
12
1_555
F
DC
24
F
N4
DC
6
1_555
hydrog
WATSON-CRICK
E
DA
13
E
N1
DA
13
1_555
F
DT
23
F
N3
DT
5
1_555
hydrog
WATSON-CRICK
E
DA
13
E
N6
DA
13
1_555
F
DT
23
F
O4
DT
5
1_555
hydrog
WATSON-CRICK
E
DT
14
E
N3
DT
14
1_555
F
DA
22
F
N1
DA
4
1_555
hydrog
WATSON-CRICK
E
DT
14
E
O4
DT
14
1_555
F
DA
22
F
N6
DA
4
1_555
hydrog
WATSON-CRICK
E
DT
15
E
N3
DT
15
1_555
F
DA
21
F
N1
DA
3
1_555
hydrog
WATSON-CRICK
E
DT
15
E
O4
DT
15
1_555
F
DA
21
F
N6
DA
3
1_555
hydrog
WATSON-CRICK
E
DA
16
E
N1
DA
16
1_555
F
DT
20
F
N3
DT
2
1_555
hydrog
WATSON-CRICK
E
DA
16
E
N6
DA
16
1_555
F
DT
20
F
O4
DT
2
1_555
hydrog
WATSON-CRICK
E
DG
17
E
N1
DG
17
1_555
F
DC
19
F
N3
DC
1
1_555
hydrog
WATSON-CRICK
E
DG
17
E
N2
DG
17
1_555
F
DC
19
F
O2
DC
1
1_555
hydrog
WATSON-CRICK
E
DG
17
E
O6
DG
17
1_555
F
DC
19
F
N4
DC
1
1_555
hydrog
TYPE_4_PAIR
F
DG
36
F
N2
DG
18
1_555
G
DG
1
G
N3
DG
1
1_555
hydrog
TYPE_4_PAIR
F
DG
36
F
N3
DG
18
1_555
G
DG
1
G
N2
DG
1
1_555
hydrog
WATSON-CRICK
G
DG
1
G
N1
DG
1
1_555
H
DC
35
H
N3
DC
17
1_555
hydrog
WATSON-CRICK
G
DG
1
G
N2
DG
1
1_555
H
DC
35
H
O2
DC
17
1_555
hydrog
WATSON-CRICK
G
DG
1
G
O6
DG
1
1_555
H
DC
35
H
N4
DC
17
1_555
hydrog
WATSON-CRICK
G
DA
2
G
N1
DA
2
1_555
H
DT
34
H
N3
DT
16
1_555
hydrog
WATSON-CRICK
G
DA
2
G
N6
DA
2
1_555
H
DT
34
H
O4
DT
16
1_555
hydrog
DA-DT PAIR
G
DA
3
G
N1
DA
3
1_555
H
DT
33
H
N3
DT
15
1_555
hydrog
DT-DA PAIR
G
DT
4
G
N3
DT
4
1_555
H
DA
32
H
N1
DA
14
1_555
DNA BINDING PROTEIN/DNA
DNA BINDING PROTEIN-DNA COMPLEX, RIBBON-HELIX-HELIX, RHH, METJ/ARC SUPERFAMILY, COOPERATIVE DNA BINDING, INC18 FAMILY
given
-0.811700
-0.520090
0.265800
-0.543280
0.505220
-0.670520
0.214440
-0.688670
-0.692640
-27.64397
-14.37253
-10.42639
given
-0.049340
0.828370
-0.558000
-0.993300
0.017740
0.114180
0.104480
0.559890
0.821950
-23.72695
-9.27670
23.01543
given
-0.537710
0.819060
-0.200020
0.828270
0.468800
-0.306910
-0.157610
-0.330690
-0.930490
-28.82347
17.26773
4.42905
2BNZ
PDB
1
2BNZ
Q57468_STRPY
UNP
1
Q57468
2BNZ
PDB
2
2BNZ
2BNZ
PDB
3
2BNZ
19
19
2BNZ
19
19
2BNZ
A
1
1
1
20
71
2BNZ
20
71
Q57468
A
2
2
53
19
19
2BNZ
19
19
2BNZ
B
1
1
1
20
71
2BNZ
20
71
Q57468
B
2
2
53
19
19
2BNZ
19
19
2BNZ
C
1
1
1
20
71
2BNZ
20
71
Q57468
C
2
2
53
19
19
2BNZ
19
19
2BNZ
D
1
1
1
20
71
2BNZ
20
71
Q57468
D
2
2
53
1
18
2BNZ
1
18
2BNZ
E
3
1
18
19
36
2BNZ
19
36
2BNZ
F
4
1
18
1
18
2BNZ
1
18
2BNZ
G
3
1
11
19
36
2BNZ
19
36
2BNZ
H
4
1
18
2
2
anti-parallel
anti-parallel
A
ASP
27
A
ASP
9
A
ARG
33
A
ARG
15
B
ASP
27
B
ASP
9
B
ARG
33
B
ARG
15
C
ASP
27
C
ASP
9
C
ARG
33
C
ARG
15
D
ASP
27
D
ASP
9
D
ARG
33
D
ARG
15
4
P 1 21 1