0.029976
0.000000
0.000000
0.000000
0.011884
0.000000
0.000000
0.000000
0.014549
0.00000
0.00000
0.00000
Alanazi, A.
Momany, C.
Neidle, E.L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
33.360
84.146
68.734
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
Na 1
22.990
SODIUM ION
non-polymer
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
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
NA
N
251
N
N
N
252
S
C
N
253
N
C
N
254
N
O
N
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
Y
261
N
C
N
262
N
O
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
N
N
275
S
C
N
276
N
C
N
277
N
O
N
278
N
C
N
279
N
C
N
280
N
C
N
281
N
O
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
N
N
292
S
C
N
293
N
C
N
294
N
O
N
295
N
C
N
296
N
O
N
297
N
O
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
N
N
306
S
C
N
307
N
C
N
308
N
O
N
309
R
C
N
310
N
O
N
311
N
C
N
312
N
O
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
N
N
323
S
C
N
324
N
C
N
325
N
O
N
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
C
Y
330
N
C
Y
331
N
C
Y
332
N
C
N
333
N
O
N
334
N
O
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
N
N
347
S
C
N
348
N
C
N
349
N
O
N
350
N
C
N
351
N
C
N
352
N
C
N
353
N
O
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
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
doub
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
doub
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
doub
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
doub
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
doub
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
doub
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
doub
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
doub
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
Y
317
N
doub
Y
318
N
sing
Y
319
N
sing
N
320
N
sing
Y
321
N
doub
N
322
N
sing
Y
323
N
doub
N
324
N
sing
Y
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
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
Crystal structure of the unbound LysR-type transcriptional regulator BenM DNA binding domain
2013
10.2210/pdb3m1e/pdb
pdb_00003m1e
100
1
2007-11-18
MAR
SINGLE WAVELENGTH
M
x-ray
1
1.0080
1.0
19-ID
APS
1.0080
SYNCHROTRON
APS BEAMLINE 19-ID
10937.559
HTH-type transcriptional regulator benM
DNA BINDING DOMAIN
1
man
polymer
22.990
SODIUM ION
1
syn
non-polymer
18.015
water
97
nat
water
Ben and cat operon transcriptional regulator
no
no
MELRHLRYFVAVVEEQSFTKAADKLCIAQPPLSRQIQNLEEELGIQLLERGSRPVKTTPEGHFFYQYAIKLLSNVDQMVS
MTKRIASGHHHHHH
MELRHLRYFVAVVEEQSFTKAADKLCIAQPPLSRQIQNLEEELGIQLLERGSRPVKTTPEGHFFYQYAIKLLSNVDQMVS
MTKRIASGHHHHHH
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
ADP1
sample
ACIAD1435, benM, benR
62977
Acinetobacter sp. ADP1
469008
Escherichia coli
BL21(DE3)RIL
plasmid
pET21B
1
2.21
44.22
MICROBATCH UNDER OIL
7.5
Equal volumes of precipitant and protein solution. Precipitant:Crystal Screen 2 # 30 - 0.1 M HEPES pH 7.5, 10% PEG 6000, 5% MPD. Protein: 20 mM Tris base (pH 8.0), 0.5 M NaCl, 10% glycerol, 150 mM imidazole, 10 mM BME, MICROBATCH UNDER OIL, temperature 288K
288
software
chem_comp_atom
chem_comp_bond
database_2
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Database references
Refinement description
Data collection
Database references
Derived calculations
1
0
2011-04-27
1
1
2011-07-13
1
2
2013-07-10
1
3
2017-11-08
1
4
2024-02-21
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2010-03-04
REL
REL
NA
SODIUM ION
HOH
water
NA
1
2
NA
NA
95
A
HOH
4
3
HOH
HOH
96
A
HOH
5
3
HOH
HOH
97
A
HOH
7
3
HOH
HOH
98
A
HOH
10
3
HOH
HOH
99
A
HOH
100
3
HOH
HOH
100
A
HOH
101
3
HOH
HOH
101
A
HOH
102
3
HOH
HOH
102
A
HOH
12
3
HOH
HOH
103
A
HOH
13
3
HOH
HOH
104
A
HOH
14
3
HOH
HOH
105
A
HOH
15
3
HOH
HOH
106
A
HOH
17
3
HOH
HOH
107
A
HOH
18
3
HOH
HOH
108
A
HOH
109
3
HOH
HOH
109
A
HOH
110
3
HOH
HOH
110
A
HOH
21
3
HOH
HOH
111
A
HOH
37
3
HOH
HOH
112
A
HOH
42
3
HOH
HOH
113
A
HOH
46
3
HOH
HOH
114
A
HOH
49
3
HOH
HOH
115
A
HOH
116
3
HOH
HOH
116
A
HOH
53
3
HOH
HOH
117
A
HOH
118
3
HOH
HOH
118
A
HOH
54
3
HOH
HOH
119
A
HOH
55
3
HOH
HOH
120
A
HOH
56
3
HOH
HOH
121
A
HOH
57
3
HOH
HOH
122
A
HOH
58
3
HOH
HOH
123
A
HOH
59
3
HOH
HOH
124
A
HOH
61
3
HOH
HOH
125
A
HOH
62
3
HOH
HOH
126
A
HOH
63
3
HOH
HOH
127
A
HOH
128
3
HOH
HOH
128
A
HOH
64
3
HOH
HOH
129
A
HOH
65
3
HOH
HOH
130
A
HOH
131
3
HOH
HOH
131
A
HOH
70
3
HOH
HOH
132
A
HOH
133
3
HOH
HOH
133
A
HOH
71
3
HOH
HOH
134
A
HOH
73
3
HOH
HOH
135
A
HOH
136
3
HOH
HOH
136
A
HOH
137
3
HOH
HOH
137
A
HOH
138
3
HOH
HOH
138
A
HOH
139
3
HOH
HOH
139
A
HOH
140
3
HOH
HOH
140
A
HOH
74
3
HOH
HOH
141
A
HOH
142
3
HOH
HOH
142
A
HOH
143
3
HOH
HOH
143
A
HOH
144
3
HOH
HOH
144
A
HOH
77
3
HOH
HOH
145
A
HOH
146
3
HOH
HOH
146
A
HOH
147
3
HOH
HOH
147
A
HOH
78
3
HOH
HOH
148
A
HOH
149
3
HOH
HOH
149
A
HOH
150
3
HOH
HOH
150
A
HOH
79
3
HOH
HOH
151
A
HOH
152
3
HOH
HOH
152
A
HOH
153
3
HOH
HOH
153
A
HOH
80
3
HOH
HOH
154
A
HOH
81
3
HOH
HOH
155
A
HOH
156
3
HOH
HOH
156
A
HOH
82
3
HOH
HOH
157
A
HOH
84
3
HOH
HOH
158
A
HOH
85
3
HOH
HOH
159
A
HOH
160
3
HOH
HOH
160
A
HOH
161
3
HOH
HOH
161
A
HOH
162
3
HOH
HOH
162
A
HOH
163
3
HOH
HOH
163
A
HOH
87
3
HOH
HOH
164
A
HOH
165
3
HOH
HOH
165
A
HOH
166
3
HOH
HOH
166
A
HOH
167
3
HOH
HOH
167
A
HOH
168
3
HOH
HOH
168
A
HOH
169
3
HOH
HOH
169
A
HOH
170
3
HOH
HOH
170
A
HOH
171
3
HOH
HOH
171
A
HOH
88
3
HOH
HOH
172
A
HOH
173
3
HOH
HOH
173
A
HOH
89
3
HOH
HOH
174
A
HOH
175
3
HOH
HOH
175
A
HOH
176
3
HOH
HOH
176
A
HOH
177
3
HOH
HOH
177
A
HOH
178
3
HOH
HOH
178
A
HOH
179
3
HOH
HOH
179
A
HOH
180
3
HOH
HOH
180
A
HOH
181
3
HOH
HOH
181
A
HOH
182
3
HOH
HOH
182
A
HOH
91
3
HOH
HOH
183
A
HOH
184
3
HOH
HOH
184
A
HOH
185
3
HOH
HOH
185
A
HOH
186
3
HOH
HOH
186
A
HOH
187
3
HOH
HOH
187
A
HOH
188
3
HOH
HOH
188
A
HOH
189
3
HOH
HOH
189
A
HOH
190
3
HOH
HOH
190
A
HOH
92
3
HOH
HOH
191
A
HOH
93
3
HOH
HOH
192
A
MET
1
n
1
MET
1
A
GLU
2
n
2
GLU
2
A
LEU
3
n
3
LEU
3
A
ARG
4
n
4
ARG
4
A
HIS
5
n
5
HIS
5
A
LEU
6
n
6
LEU
6
A
ARG
7
n
7
ARG
7
A
TYR
8
n
8
TYR
8
A
PHE
9
n
9
PHE
9
A
VAL
10
n
10
VAL
10
A
ALA
11
n
11
ALA
11
A
VAL
12
n
12
VAL
12
A
VAL
13
n
13
VAL
13
A
GLU
14
n
14
GLU
14
A
GLU
15
n
15
GLU
15
A
GLN
16
n
16
GLN
16
A
SER
17
n
17
SER
17
A
PHE
18
n
18
PHE
18
A
THR
19
n
19
THR
19
A
LYS
20
n
20
LYS
20
A
ALA
21
n
21
ALA
21
A
ALA
22
n
22
ALA
22
A
ASP
23
n
23
ASP
23
A
LYS
24
n
24
LYS
24
A
LEU
25
n
25
LEU
25
A
CYS
26
n
26
CYS
26
A
ILE
27
n
27
ILE
27
A
ALA
28
n
28
ALA
28
A
GLN
29
n
29
GLN
29
A
PRO
30
n
30
PRO
30
A
PRO
31
n
31
PRO
31
A
LEU
32
n
32
LEU
32
A
SER
33
n
33
SER
33
A
ARG
34
n
34
ARG
34
A
GLN
35
n
35
GLN
35
A
ILE
36
n
36
ILE
36
A
GLN
37
n
37
GLN
37
A
ASN
38
n
38
ASN
38
A
LEU
39
n
39
LEU
39
A
GLU
40
n
40
GLU
40
A
GLU
41
n
41
GLU
41
A
GLU
42
n
42
GLU
42
A
LEU
43
n
43
LEU
43
A
GLY
44
n
44
GLY
44
A
ILE
45
n
45
ILE
45
A
GLN
46
n
46
GLN
46
A
LEU
47
n
47
LEU
47
A
LEU
48
n
48
LEU
48
A
GLU
49
n
49
GLU
49
A
ARG
50
n
50
ARG
50
A
GLY
51
n
51
GLY
51
A
SER
52
n
52
SER
52
A
ARG
53
n
53
ARG
53
A
PRO
54
n
54
PRO
54
A
VAL
55
n
55
VAL
55
A
LYS
56
n
56
LYS
56
A
THR
57
n
57
THR
57
A
THR
58
n
58
THR
58
A
PRO
59
n
59
PRO
59
A
GLU
60
n
60
GLU
60
A
GLY
61
n
61
GLY
61
A
HIS
62
n
62
HIS
62
A
PHE
63
n
63
PHE
63
A
PHE
64
n
64
PHE
64
A
TYR
65
n
65
TYR
65
A
GLN
66
n
66
GLN
66
A
TYR
67
n
67
TYR
67
A
ALA
68
n
68
ALA
68
A
ILE
69
n
69
ILE
69
A
LYS
70
n
70
LYS
70
A
LEU
71
n
71
LEU
71
A
LEU
72
n
72
LEU
72
A
SER
73
n
73
SER
73
A
ASN
74
n
74
ASN
74
A
VAL
75
n
75
VAL
75
A
ASP
76
n
76
ASP
76
A
GLN
77
n
77
GLN
77
A
MET
78
n
78
MET
78
A
VAL
79
n
79
VAL
79
A
SER
80
n
80
SER
80
A
MET
81
n
81
MET
81
A
THR
82
n
82
THR
82
A
LYS
83
n
83
LYS
83
A
ARG
84
n
84
ARG
84
A
ILE
85
n
85
ILE
85
A
ALA
86
n
86
ALA
86
A
SER
87
n
87
SER
87
A
n
88
88
A
n
89
89
A
n
90
90
A
n
91
91
A
n
92
92
A
n
93
93
A
n
94
94
A
1.1267
-0.1633
-0.7001
2.3231
2.8307
4.4060
0.0026
0.0005
-0.0473
0.0180
-0.0068
-0.0137
0.0420
0.0468
0.0042
0.0574
-0.0017
-0.0128
0.0622
-0.0185
0.0282
refined
6.9260
-11.8290
8.5020
X-RAY DIFFRACTION
A
1
A
87
X-RAY DIFFRACTION
1
author_and_software_defined_assembly
PISA
2
dimeric
2540
-42
9260
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
3_555
-x,y,-z+1/2
crystal symmetry operation
0.0000000000
0.0000000000
34.3670000000
1
A
HOH
189
C
HOH
1
A
GLY
88
A
GLY
88
1
Y
1
A
HIS
89
A
HIS
89
1
Y
1
A
HIS
90
A
HIS
90
1
Y
1
A
HIS
91
A
HIS
91
1
Y
1
A
HIS
92
A
HIS
92
1
Y
1
A
HIS
93
A
HIS
93
1
Y
1
A
HIS
94
A
HIS
94
1
Y
32.037
0.45
0.00
0.00
0.00
0.00
-0.45
0.960
0.935
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
0.23367
0.18547
0.18778
1.80
42.07
437
8754
4.8
98.85
1.00
0.50
7.255
0.098
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.132
0.131
0.80
0.80
1.40
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
1.80
42.07
97
802
1
0
704
0.006
0.022
737
0.917
1.984
994
3.438
5.000
92
30.840
23.824
34
13.434
15.000
145
16.431
15.000
6
0.057
0.200
114
0.004
0.021
542
0.720
2.000
11
1.503
5.000
18
3.096
7.000
8
3.739
10.000
6
0.293
0.276
1.848
32
577
20
90.22
1.80
42.07
3M1E
9300
1
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
5.5.0072
data extraction
PDB
help@deposit.rcsb.org
Jan. 22, 2010
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.100
data reduction
DENZO
data scaling
SCALEPACK
Crystal Structure of BenM_DBD
1
N
N
2
N
N
3
N
N
A
GLU
2
A
GLU
2
HELX_P
A
GLN
16
A
GLN
16
1
1
15
A
SER
17
A
SER
17
HELX_P
A
LEU
25
A
LEU
25
1
2
9
A
ALA
28
A
ALA
28
HELX_P
A
GLY
44
A
GLY
44
1
3
17
A
THR
58
A
THR
58
HELX_P
A
SER
87
A
SER
87
1
4
30
metalc
1.997
A
GLU
2
A
OE1
GLU
2
1_555
A
NA
95
B
NA
NA
1_555
Transcription regulator
wHTH, Activator, Aromatic hydrocarbons catabolism, DNA-binding, Transcription, Transcription regulation, Transcription regulator
A
ARG
53
A
ARG
53
1
A
PRO
54
A
PRO
54
-2.58
BENM_ACIAD
UNP
1
1
O68014
MELRHLRYFVAVVEEQSFTKAADKLCIAQPPLSRQIQNLEEELGIQLLERGSRPVKTTPEGHFFYQYAIKLLSNVDQMVS
MTKRIAS
1
87
3M1E
1
87
O68014
A
1
1
87
1
expression tag
GLY
88
3M1E
A
O68014
UNP
88
1
expression tag
HIS
89
3M1E
A
O68014
UNP
89
1
expression tag
HIS
90
3M1E
A
O68014
UNP
90
1
expression tag
HIS
91
3M1E
A
O68014
UNP
91
1
expression tag
HIS
92
3M1E
A
O68014
UNP
92
1
expression tag
HIS
93
3M1E
A
O68014
UNP
93
1
expression tag
HIS
94
3M1E
A
O68014
UNP
94
BINDING SITE FOR RESIDUE NA A 95
A
NA
95
Software
4
A
GLU
2
A
GLU
2
4
1_555
A
GLU
2
A
GLU
2
4
3_555
A
LEU
3
A
LEU
3
4
1_555
A
LEU
3
A
LEU
3
4
3_555
20
C 2 2 21