0.015775
0.009108
0.000000
0.000000
0.018216
0.000000
0.000000
0.000000
0.009101
0.00000
0.00000
0.00000
D'Aquino, J.A.
Ringe, D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
63.390
63.390
109.872
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
C2 H6 O S
78.133
BETA-MERCAPTOETHANOL
non-polymer
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
C
N
75
N
C
N
76
N
O
N
77
N
S
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
N
N
85
R
C
N
86
N
C
N
87
N
O
N
88
N
C
N
89
N
S
N
90
N
O
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
N
N
99
S
C
N
100
N
C
N
101
N
O
N
102
N
C
N
103
N
C
N
104
N
C
N
105
N
O
N
106
N
N
N
107
N
O
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
N
N
119
S
C
N
120
N
C
N
121
N
O
N
122
N
C
N
123
N
C
N
124
N
C
N
125
N
O
N
126
N
O
N
127
N
O
N
128
N
H
N
129
N
H
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
N
N
138
N
C
N
139
N
C
N
140
N
O
N
141
N
O
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
N
N
148
S
C
N
149
N
C
N
150
N
O
N
151
N
C
Y
152
N
C
Y
153
N
N
Y
154
N
C
Y
155
N
C
Y
156
N
N
N
157
N
O
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
O
N
169
N
H
N
170
N
H
N
171
N
N
N
172
S
C
N
173
N
C
N
174
N
O
N
175
S
C
N
176
N
C
N
177
N
C
N
178
N
C
N
179
N
O
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
N
N
194
S
C
N
195
N
C
N
196
N
O
N
197
N
C
N
198
N
C
N
199
N
C
N
200
N
C
N
201
N
O
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
N
N
216
S
C
N
217
N
C
N
218
N
O
N
219
N
C
N
220
N
C
N
221
N
C
N
222
N
C
N
223
N
N
N
224
N
O
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
N
N
241
S
C
N
242
N
C
N
243
N
O
N
244
N
C
N
245
N
C
N
246
N
S
N
247
N
C
N
248
N
O
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
N
N
261
S
C
N
262
N
C
N
263
N
O
N
264
N
C
Y
265
N
C
Y
266
N
C
Y
267
N
C
Y
268
N
C
Y
269
N
C
Y
270
N
C
N
271
N
O
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
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
N
N
284
S
C
N
285
N
C
N
286
N
O
N
287
N
C
N
288
N
C
N
289
N
C
N
290
N
O
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
N
N
301
S
C
N
302
N
C
N
303
N
O
N
304
N
C
N
305
N
O
N
306
N
O
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
H
N
314
N
N
N
315
S
C
N
316
N
C
N
317
N
O
N
318
R
C
N
319
N
O
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
N
N
332
S
C
N
333
N
C
N
334
N
O
N
335
N
C
Y
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
N
Y
340
N
C
Y
341
N
C
Y
342
N
C
Y
343
N
C
Y
344
N
C
N
345
N
O
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
N
N
359
S
C
N
360
N
C
N
361
N
O
N
362
N
C
Y
363
N
C
Y
364
N
C
Y
365
N
C
Y
366
N
C
Y
367
N
C
Y
368
N
C
N
369
N
O
N
370
N
O
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
H
N
381
N
H
N
382
N
N
N
383
S
C
N
384
N
C
N
385
N
O
N
386
N
C
N
387
N
C
N
388
N
C
N
389
N
O
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
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
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
doub
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
doub
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
doub
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
doub
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
doub
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
sing
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
doub
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
Y
149
N
sing
Y
150
N
doub
Y
151
N
doub
N
152
N
sing
Y
153
N
sing
N
154
N
sing
Y
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
doub
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
doub
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
doub
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
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
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
doub
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
Y
257
N
doub
Y
258
N
sing
Y
259
N
sing
N
260
N
sing
Y
261
N
doub
N
262
N
sing
Y
263
N
doub
N
264
N
sing
Y
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
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
doub
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
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
doub
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
doub
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
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
doub
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
Y
326
N
doub
Y
327
N
sing
Y
328
N
sing
N
329
N
sing
Y
330
N
doub
Y
331
N
sing
Y
332
N
sing
N
333
N
sing
Y
334
N
sing
Y
335
N
doub
N
336
N
sing
Y
337
N
doub
N
338
N
sing
Y
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
doub
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
Y
354
N
doub
Y
355
N
sing
Y
356
N
sing
N
357
N
sing
Y
358
N
doub
N
359
N
sing
Y
360
N
doub
N
361
N
sing
Y
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
doub
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
US
J.Bacteriol.
JOBAAY
0767
0021-9193
185
4081
4086
10.1128/JB.185.14.4081-4086.2003
12837782
Determinants of the SRC homology domain 3-like fold.
2003
10.2210/pdb1p92/pdb
pdb_00001p92
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
277
1
mirrors
IMAGE PLATE
2001-11-05
RIGAKU RAXIS IV
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU
25282.727
Diphtheria toxin repressor
H79A
1
man
polymer
78.133
BETA-MERCAPTOETHANOL
1
syn
non-polymer
18.015
water
99
nat
water
Iron-dependent diphtheria tox regulatory element, Tox regulatory factor
no
no
MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKAR
LAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAAPGTRVIDAATSMP
RKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL
MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKAR
LAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAAPGTRVIDAATSMP
RKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Corynebacterium
Escherichia
sample
DTXR
1717
Corynebacterium diphtheriae
562
Escherichia coli
1
2.54
51.22
VAPOR DIFFUSION, HANGING DROP
8.0
PEG 400, ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
database_2
struct_conn
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Derived calculations
Version format compliance
Atomic model
Database references
Derived calculations
Data collection
Refinement description
1
0
2004-05-25
1
1
2008-04-29
1
2
2011-07-13
1
3
2011-11-16
1
4
2021-10-27
1
5
2023-08-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Diphtheria Tox Repressor (C102D Mutant) Complexed With Nickel
Diphtheria Tox Repressor (C102D Mutant) Complexed With Nickel and With Tox DNA
Operator
Structures of the apo- and the metal ion-activated forms of the diphtheria tox repressor from
Corynebacterium diphtheriae
RCSB
Y
RCSB
2003-05-08
REL
REL
BME
BETA-MERCAPTOETHANOL
HOH
water
1BYM
PDB ENTRIES 1BYM, 2TDX
PDB
experimental model
2TDX
PDB ENTRIES 1BYM, 2TDX
PDB
experimental model
BME
550
2
BME
BME
550
A
HOH
1
3
HOH
HOH
551
A
HOH
2
3
HOH
HOH
552
A
HOH
3
3
HOH
HOH
553
A
HOH
4
3
HOH
HOH
554
A
HOH
5
3
HOH
HOH
555
A
HOH
6
3
HOH
HOH
556
A
HOH
7
3
HOH
HOH
557
A
HOH
8
3
HOH
HOH
558
A
HOH
9
3
HOH
HOH
559
A
HOH
10
3
HOH
HOH
560
A
HOH
11
3
HOH
HOH
561
A
HOH
12
3
HOH
HOH
562
A
HOH
13
3
HOH
HOH
563
A
HOH
14
3
HOH
HOH
564
A
HOH
15
3
HOH
HOH
565
A
HOH
16
3
HOH
HOH
566
A
HOH
17
3
HOH
HOH
567
A
HOH
18
3
HOH
HOH
568
A
HOH
19
3
HOH
HOH
569
A
HOH
20
3
HOH
HOH
570
A
HOH
21
3
HOH
HOH
571
A
HOH
22
3
HOH
HOH
572
A
HOH
23
3
HOH
HOH
573
A
HOH
24
3
HOH
HOH
574
A
HOH
25
3
HOH
HOH
575
A
HOH
26
3
HOH
HOH
576
A
HOH
27
3
HOH
HOH
577
A
HOH
28
3
HOH
HOH
578
A
HOH
29
3
HOH
HOH
579
A
HOH
30
3
HOH
HOH
580
A
HOH
31
3
HOH
HOH
581
A
HOH
32
3
HOH
HOH
582
A
HOH
33
3
HOH
HOH
583
A
HOH
34
3
HOH
HOH
584
A
HOH
35
3
HOH
HOH
585
A
HOH
36
3
HOH
HOH
586
A
HOH
37
3
HOH
HOH
587
A
HOH
38
3
HOH
HOH
588
A
HOH
39
3
HOH
HOH
589
A
HOH
40
3
HOH
HOH
590
A
HOH
41
3
HOH
HOH
591
A
HOH
42
3
HOH
HOH
592
A
HOH
43
3
HOH
HOH
593
A
HOH
44
3
HOH
HOH
594
A
HOH
45
3
HOH
HOH
595
A
HOH
46
3
HOH
HOH
596
A
HOH
47
3
HOH
HOH
597
A
HOH
48
3
HOH
HOH
598
A
HOH
49
3
HOH
HOH
599
A
HOH
50
3
HOH
HOH
600
A
HOH
51
3
HOH
HOH
601
A
HOH
52
3
HOH
HOH
602
A
HOH
53
3
HOH
HOH
603
A
HOH
54
3
HOH
HOH
604
A
HOH
55
3
HOH
HOH
605
A
HOH
56
3
HOH
HOH
606
A
HOH
57
3
HOH
HOH
607
A
HOH
58
3
HOH
HOH
608
A
HOH
59
3
HOH
HOH
609
A
HOH
60
3
HOH
HOH
610
A
HOH
61
3
HOH
HOH
611
A
HOH
62
3
HOH
HOH
612
A
HOH
63
3
HOH
HOH
613
A
HOH
64
3
HOH
HOH
614
A
HOH
65
3
HOH
HOH
615
A
HOH
66
3
HOH
HOH
616
A
HOH
67
3
HOH
HOH
617
A
HOH
68
3
HOH
HOH
618
A
HOH
69
3
HOH
HOH
619
A
HOH
70
3
HOH
HOH
620
A
HOH
71
3
HOH
HOH
621
A
HOH
72
3
HOH
HOH
622
A
HOH
73
3
HOH
HOH
623
A
HOH
74
3
HOH
HOH
624
A
HOH
75
3
HOH
HOH
625
A
HOH
76
3
HOH
HOH
626
A
HOH
77
3
HOH
HOH
627
A
HOH
78
3
HOH
HOH
628
A
HOH
80
3
HOH
HOH
629
A
HOH
81
3
HOH
HOH
630
A
HOH
83
3
HOH
HOH
631
A
HOH
84
3
HOH
HOH
632
A
HOH
86
3
HOH
HOH
633
A
HOH
87
3
HOH
HOH
634
A
HOH
88
3
HOH
HOH
635
A
HOH
89
3
HOH
HOH
636
A
HOH
90
3
HOH
HOH
637
A
HOH
91
3
HOH
HOH
638
A
HOH
92
3
HOH
HOH
639
A
HOH
93
3
HOH
HOH
640
A
HOH
94
3
HOH
HOH
641
A
HOH
95
3
HOH
HOH
642
A
HOH
96
3
HOH
HOH
643
A
HOH
97
3
HOH
HOH
644
A
HOH
98
3
HOH
HOH
645
A
HOH
99
3
HOH
HOH
646
A
HOH
101
3
HOH
HOH
647
A
HOH
103
3
HOH
HOH
648
A
HOH
104
3
HOH
HOH
649
A
MET
1
n
1
MET
1
A
LYS
2
n
2
LYS
2
A
ASP
3
n
3
ASP
3
A
LEU
4
n
4
LEU
4
A
VAL
5
n
5
VAL
5
A
ASP
6
n
6
ASP
6
A
THR
7
n
7
THR
7
A
THR
8
n
8
THR
8
A
GLU
9
n
9
GLU
9
A
MET
10
n
10
MET
10
A
TYR
11
n
11
TYR
11
A
LEU
12
n
12
LEU
12
A
ARG
13
n
13
ARG
13
A
THR
14
n
14
THR
14
A
ILE
15
n
15
ILE
15
A
TYR
16
n
16
TYR
16
A
GLU
17
n
17
GLU
17
A
LEU
18
n
18
LEU
18
A
GLU
19
n
19
GLU
19
A
GLU
20
n
20
GLU
20
A
GLU
21
n
21
GLU
21
A
GLY
22
n
22
GLY
22
A
VAL
23
n
23
VAL
23
A
THR
24
n
24
THR
24
A
PRO
25
n
25
PRO
25
A
LEU
26
n
26
LEU
26
A
ARG
27
n
27
ARG
27
A
ALA
28
n
28
ALA
28
A
ARG
29
n
29
ARG
29
A
ILE
30
n
30
ILE
30
A
ALA
31
n
31
ALA
31
A
GLU
32
n
32
GLU
32
A
ARG
33
n
33
ARG
33
A
LEU
34
n
34
LEU
34
A
GLU
35
n
35
GLU
35
A
GLN
36
n
36
GLN
36
A
SER
37
n
37
SER
37
A
GLY
38
n
38
GLY
38
A
PRO
39
n
39
PRO
39
A
THR
40
n
40
THR
40
A
VAL
41
n
41
VAL
41
A
SER
42
n
42
SER
42
A
GLN
43
n
43
GLN
43
A
THR
44
n
44
THR
44
A
VAL
45
n
45
VAL
45
A
ALA
46
n
46
ALA
46
A
ARG
47
n
47
ARG
47
A
MET
48
n
48
MET
48
A
GLU
49
n
49
GLU
49
A
ARG
50
n
50
ARG
50
A
ASP
51
n
51
ASP
51
A
GLY
52
n
52
GLY
52
A
LEU
53
n
53
LEU
53
A
VAL
54
n
54
VAL
54
A
VAL
55
n
55
VAL
55
A
VAL
56
n
56
VAL
56
A
ALA
57
n
57
ALA
57
A
SER
58
n
58
SER
58
A
ASP
59
n
59
ASP
59
A
ARG
60
n
60
ARG
60
A
SER
61
n
61
SER
61
A
LEU
62
n
62
LEU
62
A
GLN
63
n
63
GLN
63
A
MET
64
n
64
MET
64
A
THR
65
n
65
THR
65
A
PRO
66
n
66
PRO
66
A
THR
67
n
67
THR
67
A
GLY
68
n
68
GLY
68
A
ARG
69
n
69
ARG
69
A
THR
70
n
70
THR
70
A
LEU
71
n
71
LEU
71
A
ALA
72
n
72
ALA
72
A
THR
73
n
73
THR
73
A
ALA
74
n
74
ALA
74
A
VAL
75
n
75
VAL
75
A
MET
76
n
76
MET
76
A
ARG
77
n
77
ARG
77
A
LYS
78
n
78
LYS
78
A
ALA
79
n
79
ALA
79
A
ARG
80
n
80
ARG
80
A
LEU
81
n
81
LEU
81
A
ALA
82
n
82
ALA
82
A
GLU
83
n
83
GLU
83
A
ARG
84
n
84
ARG
84
A
LEU
85
n
85
LEU
85
A
LEU
86
n
86
LEU
86
A
THR
87
n
87
THR
87
A
ASP
88
n
88
ASP
88
A
ILE
89
n
89
ILE
89
A
ILE
90
n
90
ILE
90
A
GLY
91
n
91
GLY
91
A
LEU
92
n
92
LEU
92
A
ASP
93
n
93
ASP
93
A
ILE
94
n
94
ILE
94
A
ASN
95
n
95
ASN
95
A
LYS
96
n
96
LYS
96
A
VAL
97
n
97
VAL
97
A
HIS
98
n
98
HIS
98
A
ASP
99
n
99
ASP
99
A
GLU
100
n
100
GLU
100
A
ALA
101
n
101
ALA
101
A
CYS
102
n
102
CYS
102
A
ARG
103
n
103
ARG
103
A
TRP
104
n
104
TRP
104
A
GLU
105
n
105
GLU
105
A
HIS
106
n
106
HIS
106
A
VAL
107
n
107
VAL
107
A
MET
108
n
108
MET
108
A
SER
109
n
109
SER
109
A
ASP
110
n
110
ASP
110
A
GLU
111
n
111
GLU
111
A
VAL
112
n
112
VAL
112
A
GLU
113
n
113
GLU
113
A
ARG
114
n
114
ARG
114
A
ARG
115
n
115
ARG
115
A
LEU
116
n
116
LEU
116
A
VAL
117
n
117
VAL
117
A
LYS
118
n
118
LYS
118
A
VAL
119
n
119
VAL
119
A
LEU
120
n
120
LEU
120
A
LYS
121
n
121
LYS
121
A
ASP
122
n
122
ASP
122
A
VAL
123
n
123
VAL
123
A
SER
124
n
124
SER
124
A
ARG
125
n
125
ARG
125
A
SER
126
n
126
SER
126
A
PRO
127
n
127
PRO
127
A
PHE
128
n
128
PHE
128
A
GLY
129
n
129
GLY
129
A
ASN
130
n
130
ASN
130
A
PRO
131
n
131
PRO
131
A
ILE
132
n
132
ILE
132
A
PRO
133
n
133
PRO
133
A
GLY
134
n
134
GLY
134
A
LEU
135
n
135
LEU
135
A
ASP
136
n
136
ASP
136
A
GLU
137
n
137
GLU
137
A
LEU
138
n
138
LEU
138
A
GLY
139
n
139
GLY
139
A
n
140
140
A
n
141
141
A
n
142
142
A
n
143
143
A
n
144
144
A
n
145
145
A
n
146
146
A
n
147
147
A
PRO
148
n
148
PRO
148
A
GLY
149
n
149
GLY
149
A
THR
150
n
150
THR
150
A
ARG
151
n
151
ARG
151
A
VAL
152
n
152
VAL
152
A
ILE
153
n
153
ILE
153
A
ASP
154
n
154
ASP
154
A
ALA
155
n
155
ALA
155
A
ALA
156
n
156
ALA
156
A
THR
157
n
157
THR
157
A
SER
158
n
158
SER
158
A
MET
159
n
159
MET
159
A
PRO
160
n
160
PRO
160
A
ARG
161
n
161
ARG
161
A
ALA
162
n
162
LYS
162
A
VAL
163
n
163
VAL
163
A
ALA
164
n
164
ARG
164
A
ILE
165
n
165
ILE
165
A
VAL
166
n
166
VAL
166
A
GLN
167
n
167
GLN
167
A
ILE
168
n
168
ILE
168
A
ASN
169
n
169
ASN
169
A
GLU
170
n
170
GLU
170
A
ILE
171
n
171
ILE
171
A
PHE
172
n
172
PHE
172
A
GLN
173
n
173
GLN
173
A
VAL
174
n
174
VAL
174
A
GLU
175
n
175
GLU
175
A
THR
176
n
176
THR
176
A
ASP
177
n
177
ASP
177
A
GLN
178
n
178
GLN
178
A
PHE
179
n
179
PHE
179
A
THR
180
n
180
THR
180
A
GLN
181
n
181
GLN
181
A
LEU
182
n
182
LEU
182
A
LEU
183
n
183
LEU
183
A
ASP
184
n
184
ASP
184
A
ALA
185
n
185
ALA
185
A
ASP
186
n
186
ASP
186
A
ILE
187
n
187
ILE
187
A
ALA
188
n
188
ARG
188
A
VAL
189
n
189
VAL
189
A
GLY
190
n
190
GLY
190
A
SER
191
n
191
SER
191
A
ALA
192
n
192
GLU
192
A
VAL
193
n
193
VAL
193
A
ALA
194
n
194
GLU
194
A
ALA
195
n
195
ILE
195
A
VAL
196
n
196
VAL
196
A
ASP
197
n
197
ASP
197
A
ARG
198
n
198
ARG
198
A
ASP
199
n
199
ASP
199
A
GLY
200
n
200
GLY
200
A
HIS
201
n
201
HIS
201
A
ILE
202
n
202
ILE
202
A
THR
203
n
203
THR
203
A
LEU
204
n
204
LEU
204
A
SER
205
n
205
SER
205
A
HIS
206
n
206
HIS
206
A
ASN
207
n
207
ASN
207
A
GLY
208
n
208
GLY
208
A
ALA
209
n
209
LYS
209
A
ASP
210
n
210
ASP
210
A
VAL
211
n
211
VAL
211
A
GLU
212
n
212
GLU
212
A
LEU
213
n
213
LEU
213
A
LEU
214
n
214
LEU
214
A
ASP
215
n
215
ASP
215
A
ASP
216
n
216
ASP
216
A
LEU
217
n
217
LEU
217
A
ALA
218
n
218
ALA
218
A
HIS
219
n
219
HIS
219
A
THR
220
n
220
THR
220
A
ILE
221
n
221
ILE
221
A
ARG
222
n
222
ARG
222
A
ILE
223
n
223
ILE
223
A
GLU
224
n
224
GLU
224
A
GLU
225
n
225
GLU
225
A
LEU
226
n
226
LEU
226
A
author_defined_assembly
1
monomeric
software_defined_assembly
PISA,PQS
2
dimeric
2740
-22
22840
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
-0.5000000000
-0.8660254038
0.0000000000
-0.8660254038
0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
6_765
-x+2,-x+y+1,-z+1/3
crystal symmetry operation
95.0850000000
54.8973503459
36.6240000000
A
N
VAL
55
A
N
VAL
55
A
O
GLN
63
A
O
GLN
63
A
N
THR
150
A
N
THR
150
A
O
ILE
223
A
O
ILE
223
1
A
HOH
618
C
HOH
1
A
N
PRO
148
A
N
PRO
148
0
Y
1
A
CA
PRO
148
A
CA
PRO
148
0
Y
1
A
C
PRO
148
A
C
PRO
148
0
Y
1
A
O
PRO
148
A
O
PRO
148
0
Y
1
A
CB
PRO
148
A
CB
PRO
148
0
Y
1
A
CG
LYS
162
A
CG
LYS
162
1
Y
1
A
CD
LYS
162
A
CD
LYS
162
1
Y
1
A
CE
LYS
162
A
CE
LYS
162
1
Y
1
A
NZ
LYS
162
A
NZ
LYS
162
1
Y
1
A
CG
ARG
164
A
CG
ARG
164
1
Y
1
A
CD
ARG
164
A
CD
ARG
164
1
Y
1
A
NE
ARG
164
A
NE
ARG
164
1
Y
1
A
CZ
ARG
164
A
CZ
ARG
164
1
Y
1
A
NH1
ARG
164
A
NH1
ARG
164
1
Y
1
A
NH2
ARG
164
A
NH2
ARG
164
1
Y
1
A
CG
ARG
188
A
CG
ARG
188
1
Y
1
A
CD
ARG
188
A
CD
ARG
188
1
Y
1
A
NE
ARG
188
A
NE
ARG
188
1
Y
1
A
CZ
ARG
188
A
CZ
ARG
188
1
Y
1
A
NH1
ARG
188
A
NH1
ARG
188
1
Y
1
A
NH2
ARG
188
A
NH2
ARG
188
1
Y
1
A
CG
GLU
192
A
CG
GLU
192
1
Y
1
A
CD
GLU
192
A
CD
GLU
192
1
Y
1
A
OE1
GLU
192
A
OE1
GLU
192
1
Y
1
A
OE2
GLU
192
A
OE2
GLU
192
1
Y
1
A
CG
GLU
194
A
CG
GLU
194
1
Y
1
A
CD
GLU
194
A
CD
GLU
194
1
Y
1
A
OE1
GLU
194
A
OE1
GLU
194
1
Y
1
A
OE2
GLU
194
A
OE2
GLU
194
1
Y
1
A
CG1
ILE
195
A
CG1
ILE
195
1
Y
1
A
CG2
ILE
195
A
CG2
ILE
195
1
Y
1
A
CD1
ILE
195
A
CD1
ILE
195
1
Y
1
A
CG
LYS
209
A
CG
LYS
209
1
Y
1
A
CD
LYS
209
A
CD
LYS
209
1
Y
1
A
CE
LYS
209
A
CE
LYS
209
1
Y
1
A
NZ
LYS
209
A
NZ
LYS
209
1
Y
1
A
VAL
140
A
VAL
140
1
Y
1
A
GLY
141
A
GLY
141
1
Y
1
A
ASN
142
A
ASN
142
1
Y
1
A
SER
143
A
SER
143
1
Y
1
A
ASP
144
A
ASP
144
1
Y
1
A
ALA
145
A
ALA
145
1
Y
1
A
ALA
146
A
ALA
146
1
Y
1
A
ALA
147
A
ALA
147
1
Y
1
A
GLY
149
A
GLY
149
0
Y
1
A
A
C
CD
GLY
PRO
38
39
1.68
1
54.64
1.50
119.30
173.94
A
A
A
C
N
CA
GLY
PRO
PRO
38
39
39
Y
1
-55.31
2.10
128.40
73.09
A
A
A
C
N
CD
GLY
PRO
PRO
38
39
39
Y
1
A
A
O
O
GLY
THR
38
176
2.10
1_555
1_655
1
A
LYS
2
-168.20
72.18
1
A
ASP
3
175.52
42.12
1
A
LEU
4
173.60
-62.50
1
A
SER
37
107.72
96.02
1
A
PRO
39
-147.56
56.93
1
A
THR
40
-49.67
165.49
1
A
ARG
60
162.77
-2.75
1
A
THR
150
175.34
153.32
1
A
ASP
186
73.82
-98.04
1
A
ILE
187
45.37
88.28
1
A
ARG
188
-131.26
-60.56
1
A
VAL
189
-155.70
63.66
1
A
ASP
197
169.26
-97.11
1
A
ARG
198
-86.20
46.28
1
A
HIS
206
-52.01
-5.81
1
A
ILE
223
-93.10
-150.09
1
A
GLU
224
179.16
120.38
PROTEIN_REP.PARAM
PROTEIN.TOP
BME.PARAM
WATER.PARAM
42.4
-1.30
1.16
0.00
-1.30
0.00
2.60
0.28
0.010
0.243
0.243
0.243
2.10
27.45
716
15278
14509
4.9
93.9
RANDOM
272961.01
272961.01
0.000000
1
RESTRAINED
THROUGHOUT
0.0
0.0
MOLECULAR REPLACEMENT
PDB ENTRIES 1BYM, 2TDX
Engh & Huber
FLAT MODEL
67.949
0.327259
0.37
0.29
5.00
0.26
0.23
2.10
27.45
99
1791
4
0
1688
0.007
2.0
20.7
0.82
3.19
1.50
4.44
2.00
5.09
2.00
6.77
2.50
0.315
0.030
0.278
2.23
108
2066
6
5.0
86.8
16.4
2.10
30.00
1P92
15278
15278
0
0
0.078
1
12.9
2.24
98.8
refinement
CNS
1.0
data reduction
DENZO
data scaling
SCALEPACK
phasing
EPMR
Crystal Structure of (H79A)DtxR
1
N
N
2
N
N
3
N
N
A
LEU
4
A
LEU
4
HELX_P
A
GLY
22
A
GLY
22
1
1
19
A
LEU
26
A
LEU
26
HELX_P
A
GLU
35
A
GLU
35
1
2
10
A
THR
40
A
THR
40
HELX_P
A
ASP
51
A
ASP
51
1
3
12
A
THR
65
A
THR
65
HELX_P
A
ILE
89
A
ILE
89
1
4
25
A
ASP
93
A
ASP
93
HELX_P
A
GLU
105
A
GLU
105
1
5
13
A
SER
109
A
SER
109
HELX_P
A
LEU
120
A
LEU
120
1
6
12
A
GLY
134
A
GLY
134
HELX_P
A
GLY
139
A
GLY
139
1
7
6
A
VAL
152
A
VAL
152
HELX_P
A
ALA
156
A
ALA
156
1
8
5
A
ASN
169
A
ASN
169
HELX_P
A
GLN
173
A
GLN
173
5
9
5
A
ASP
177
A
ASP
177
HELX_P
A
ALA
185
A
ALA
185
1
10
9
A
LEU
214
A
LEU
214
HELX_P
A
ILE
221
A
ILE
221
1
11
8
covale
2.040
none
A
CYS
102
A
SG
CYS
102
1_555
A
BME
550
B
S2
BME
1_555
DNA BINDING PROTEIN
Diphtheria toxin repressor, DtxR, DNA-binding protein, Helix-turn-helix, SH3-like, metal ion binding site, DNA BINDING PROTEIN
DTXR_CORDI
UNP
1
1
P33120
MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHR
LAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAAPGTRVIDAATSMP
RKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL
1
226
1P92
1
226
P33120
A
1
1
226
1
HIS
engineered mutation
ALA
79
1P92
A
P33120
UNP
79
79
2
2
anti-parallel
anti-parallel
A
VAL
54
A
VAL
54
A
VAL
56
A
VAL
56
A
LEU
62
A
LEU
62
A
MET
64
A
MET
64
A
THR
150
A
THR
150
A
ARG
151
A
ARG
151
A
ARG
222
A
ARG
222
A
ILE
223
A
ILE
223
BINDING SITE FOR RESIDUE BME A 550
A
BME
550
Software
1
A
CYS
102
A
CYS
102
1
1_555
152
P 31 2 1