0.005982
0.000000
0.000000
0.000000
0.005982
0.000000
0.000000
0.000000
0.005982
0.00000
0.00000
0.00000
Cappadocia, L.
Brisson, N.
Sygusch, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
96
90.00
90.00
90.00
167.164
167.164
167.164
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 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
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
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
N
86
N
N
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
H
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
N
N
111
S
C
N
112
N
C
N
113
N
O
N
114
N
C
N
115
N
C
N
116
N
C
N
117
N
O
N
118
N
N
N
119
N
O
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
H
N
128
N
H
N
129
N
H
N
130
N
N
N
131
S
C
N
132
N
C
N
133
N
O
N
134
N
C
N
135
N
C
N
136
N
C
N
137
N
O
N
138
N
O
N
139
N
O
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
N
N
150
N
C
N
151
N
C
N
152
N
O
N
153
N
O
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
N
N
160
S
C
N
161
N
C
N
162
N
O
N
163
N
C
Y
164
N
C
Y
165
N
N
Y
166
N
C
Y
167
N
C
Y
168
N
N
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
O
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
S
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
O
N
214
N
H
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
N
N
228
S
C
N
229
N
C
N
230
N
O
N
231
N
C
N
232
N
C
N
233
N
C
N
234
N
C
N
235
N
N
N
236
N
O
N
237
N
H
N
238
N
H
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
H
N
251
N
H
N
252
N
N
N
253
S
C
N
254
N
C
N
255
N
O
N
256
N
C
N
257
N
C
N
258
N
S
N
259
N
C
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
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
N
N
273
S
C
N
274
N
C
N
275
N
O
N
276
N
C
Y
277
N
C
Y
278
N
C
Y
279
N
C
Y
280
N
C
Y
281
N
C
Y
282
N
C
N
283
N
O
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
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
N
N
296
S
C
N
297
N
C
N
298
N
O
N
299
N
C
N
300
N
C
N
301
N
C
N
302
N
O
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
O
N
318
N
O
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
N
N
327
S
C
N
328
N
C
N
329
N
O
N
330
R
C
N
331
N
O
N
332
N
C
N
333
N
O
N
334
N
H
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
N
N
344
S
C
N
345
N
C
N
346
N
O
N
347
N
C
Y
348
N
C
Y
349
N
C
Y
350
N
C
Y
351
N
N
Y
352
N
C
Y
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
N
357
N
O
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
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
N
N
371
S
C
N
372
N
C
N
373
N
O
N
374
N
C
Y
375
N
C
Y
376
N
C
Y
377
N
C
Y
378
N
C
Y
379
N
C
Y
380
N
C
N
381
N
O
N
382
N
O
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
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
N
N
395
S
C
N
396
N
C
N
397
N
O
N
398
N
C
N
399
N
C
N
400
N
C
N
401
N
O
N
402
N
H
N
403
N
H
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
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
N
93
N
sing
N
94
N
sing
N
95
N
doub
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
doub
N
100
N
sing
N
101
N
sing
N
102
N
doub
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
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
doub
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
doub
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
doub
N
133
N
sing
N
134
N
sing
N
135
N
sing
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
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
doub
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
doub
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
Y
164
N
sing
Y
165
N
doub
Y
166
N
doub
N
167
N
sing
Y
168
N
sing
N
169
N
sing
Y
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
doub
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
sing
N
201
N
sing
N
202
N
sing
N
203
N
doub
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
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
doub
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
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
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
doub
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
Y
272
N
doub
Y
273
N
sing
Y
274
N
sing
N
275
N
sing
Y
276
N
doub
N
277
N
sing
Y
278
N
doub
N
279
N
sing
Y
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
doub
N
291
N
sing
N
292
N
sing
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
sing
N
306
N
sing
N
307
N
doub
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
doub
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
Y
341
N
doub
Y
342
N
sing
Y
343
N
sing
N
344
N
sing
Y
345
N
doub
Y
346
N
sing
Y
347
N
sing
N
348
N
sing
Y
349
N
sing
Y
350
N
doub
N
351
N
sing
Y
352
N
doub
N
353
N
sing
Y
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
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
doub
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
Y
369
N
doub
Y
370
N
sing
Y
371
N
sing
N
372
N
sing
Y
373
N
doub
N
374
N
sing
Y
375
N
doub
N
376
N
sing
Y
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
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
doub
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
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
US
Plant Cell
PLCEEW
2109
1040-4651
22
1849
1867
10.1105/tpc.109.071399
20551348
Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair.
2010
10.2210/pdb3n1i/pdb
pdb_00003n1i
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2007-03-07
ADSC QUANTUM 315
SINGLE WAVELENGTH
M
x-ray
1
1.08
1.0
X29A
NSLS
1.08
SYNCHROTRON
NSLS BEAMLINE X29A
20000.715
protein StWhy2
1
man
polymer
ERE32
2692.778
DNA 32-mer ERE32
1
syn
polymer
18.015
water
36
nat
water
no
no
MADAGKREGRVFAPYSVFKGKAALSAEPRLPTFNRLDSGGVKLNRRGVIMLTFWPSVGERKYDWEKRQLFALSATEVGSL
ISMGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGYFISLSVVNNNLKTNDRFTVPVTTAEFAVMRTAFSFALPHI
MGWDRFTNRPLEHHHHHH
MADAGKREGRVFAPYSVFKGKAALSAEPRLPTFNRLDSGGVKLNRRGVIMLTFWPSVGERKYDWEKRQLFALSATEVGSL
ISMGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGYFISLSVVNNNLKTNDRFTVPVTTAEFAVMRTAFSFALPHI
MGWDRFTNRPLEHHHHHH
A
polypeptide(L)
no
no
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)
TTTTTTTTT
B
polydeoxyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Potato
Kennebec
sample
StWhy2
4113
Solanum tuberosum
469008
Escherichia coli
BL21(DE3)
plasmid
pET21a
1
2.17
47.91
VAPOR DIFFUSION, HANGING DROP
8.0
13.5% PEG6000, 0.1M Tris, 1.0M LiCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
software
struct_ref_seq
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Data collection
Database references
Refinement description
Data collection
Database references
Refinement description
1
0
2010-08-11
1
1
2011-07-13
1
2
2019-07-17
1
3
2023-09-06
_software.classification
_software.name
_software.version
_struct_ref_seq.db_align_beg
_struct_ref_seq.db_align_end
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
Crystal Structure of StWhy2
Crystal Structure of StWhy2-dT32 complex
Crystal Structure of StWhy2-cERE32 complex
Crystal Structure of StWhy2-rcERE32 complex
RCSB
Y
RCSB
2010-05-15
REL
REL
HOH
water
DNA Synthesis
sample
THE SEQUENCE OF THE CRYSTALLIZED DNA IS A 32-MER OLIGONUCLEOTIDE WITH SEQUENCE TGTCATTTTTGTCATTTTTGTCATTTTTGTCA. ONLY 9 RESIDUES OF THYMIDINE WERE MODELED IN THE COORDINATES OF THE ASYMMETRIC UNIT. ACCORDING TO THE AUTHORS, THE 32-MER DNA BINDS A TETRAMER THAT INCLUDE FOUR MONOMERS OF FOUR ASYMMETRIC UNITS; THE STWHY2-DNA BINDING IS NOT SEQUENCE SPECIFIC THUS EACH TETRAMERIC PROTEIN BINDS A 32-MER DNA IN DIFFERENT SEQUENCE REGISTERS; AS A RESULT ONLY THREE OF THE FOUR DNA-BINDING SITES OF EACH TETRAMER WOULD BE PHYSICALLY OCCUPIED BY THE DNA.
1L3A
PDB ENTRY 1L3A
PDB
experimental model
HOH
1
3
HOH
HOH
1
A
HOH
2
3
HOH
HOH
2
A
HOH
3
3
HOH
HOH
3
A
HOH
4
3
HOH
HOH
4
A
HOH
5
3
HOH
HOH
5
A
HOH
7
3
HOH
HOH
7
A
HOH
8
3
HOH
HOH
8
A
HOH
9
3
HOH
HOH
9
A
HOH
10
3
HOH
HOH
10
A
HOH
11
3
HOH
HOH
11
A
HOH
12
3
HOH
HOH
12
A
HOH
13
3
HOH
HOH
13
A
HOH
14
3
HOH
HOH
14
A
HOH
15
3
HOH
HOH
15
A
HOH
16
3
HOH
HOH
16
A
HOH
17
3
HOH
HOH
17
A
HOH
18
3
HOH
HOH
18
A
HOH
19
3
HOH
HOH
19
A
HOH
20
3
HOH
HOH
20
A
HOH
21
3
HOH
HOH
21
A
HOH
22
3
HOH
HOH
22
A
HOH
23
3
HOH
HOH
23
A
HOH
24
3
HOH
HOH
24
A
HOH
25
3
HOH
HOH
25
A
HOH
26
3
HOH
HOH
26
A
HOH
27
3
HOH
HOH
27
A
HOH
28
3
HOH
HOH
28
A
HOH
29
3
HOH
HOH
29
A
HOH
30
3
HOH
HOH
30
A
HOH
31
3
HOH
HOH
31
A
HOH
32
3
HOH
HOH
32
A
HOH
33
3
HOH
HOH
33
A
HOH
34
3
HOH
HOH
34
A
HOH
35
3
HOH
HOH
35
A
HOH
36
3
HOH
HOH
36
A
HOH
6
3
HOH
HOH
10
B
n
1
47
A
n
2
48
A
n
3
49
A
n
4
50
A
n
5
51
A
n
6
52
A
n
7
53
A
n
8
54
A
GLY
55
n
9
GLY
55
A
ARG
56
n
10
ARG
56
A
VAL
57
n
11
VAL
57
A
PHE
58
n
12
PHE
58
A
ALA
59
n
13
ALA
59
A
PRO
60
n
14
PRO
60
A
TYR
61
n
15
TYR
61
A
SER
62
n
16
SER
62
A
VAL
63
n
17
VAL
63
A
PHE
64
n
18
PHE
64
A
LYS
65
n
19
LYS
65
A
GLY
66
n
20
GLY
66
A
LYS
67
n
21
LYS
67
A
ALA
68
n
22
ALA
68
A
ALA
69
n
23
ALA
69
A
LEU
70
n
24
LEU
70
A
SER
71
n
25
SER
71
A
ALA
72
n
26
ALA
72
A
GLU
73
n
27
GLU
73
A
PRO
74
n
28
PRO
74
A
ARG
75
n
29
ARG
75
A
LEU
76
n
30
LEU
76
A
PRO
77
n
31
PRO
77
A
THR
78
n
32
THR
78
A
PHE
79
n
33
PHE
79
A
ASN
80
n
34
ASN
80
A
ARG
81
n
35
ARG
81
A
LEU
82
n
36
LEU
82
A
ASP
83
n
37
ASP
83
A
SER
84
n
38
SER
84
A
GLY
85
n
39
GLY
85
A
GLY
86
n
40
GLY
86
A
VAL
87
n
41
VAL
87
A
LYS
88
n
42
LYS
88
A
LEU
89
n
43
LEU
89
A
ASN
90
n
44
ASN
90
A
ARG
91
n
45
ARG
91
A
ARG
92
n
46
ARG
92
A
GLY
93
n
47
GLY
93
A
VAL
94
n
48
VAL
94
A
ILE
95
n
49
ILE
95
A
MET
96
n
50
MET
96
A
LEU
97
n
51
LEU
97
A
THR
98
n
52
THR
98
A
PHE
99
n
53
PHE
99
A
TRP
100
n
54
TRP
100
A
PRO
101
n
55
PRO
101
A
SER
102
n
56
SER
102
A
VAL
103
n
57
VAL
103
A
GLY
104
n
58
GLY
104
A
GLU
105
n
59
GLU
105
A
ARG
106
n
60
ARG
106
A
LYS
107
n
61
LYS
107
A
TYR
108
n
62
TYR
108
A
ASP
109
n
63
ASP
109
A
TRP
110
n
64
TRP
110
A
GLU
111
n
65
GLU
111
A
LYS
112
n
66
LYS
112
A
ARG
113
n
67
ARG
113
A
GLN
114
n
68
GLN
114
A
LEU
115
n
69
LEU
115
A
PHE
116
n
70
PHE
116
A
ALA
117
n
71
ALA
117
A
LEU
118
n
72
LEU
118
A
SER
119
n
73
SER
119
A
ALA
120
n
74
ALA
120
A
THR
121
n
75
THR
121
A
GLU
122
n
76
GLU
122
A
VAL
123
n
77
VAL
123
A
GLY
124
n
78
GLY
124
A
SER
125
n
79
SER
125
A
LEU
126
n
80
LEU
126
A
ILE
127
n
81
ILE
127
A
SER
128
n
82
SER
128
A
MET
129
n
83
MET
129
A
GLY
130
n
84
GLY
130
A
THR
131
n
85
THR
131
A
ARG
132
n
86
ARG
132
A
ASP
133
n
87
ASP
133
A
SER
134
n
88
SER
134
A
SER
135
n
89
SER
135
A
GLU
136
n
90
GLU
136
A
PHE
137
n
91
PHE
137
A
PHE
138
n
92
PHE
138
A
HIS
139
n
93
HIS
139
A
ASP
140
n
94
ASP
140
A
PRO
141
n
95
PRO
141
A
SER
142
n
96
SER
142
A
MET
143
n
97
MET
143
A
LEU
144
n
98
LEU
144
A
SER
145
n
99
SER
145
A
SER
146
n
100
SER
146
A
ASN
147
n
101
ASN
147
A
ALA
148
n
102
ALA
148
A
GLY
149
n
103
GLY
149
A
GLN
150
n
104
GLN
150
A
VAL
151
n
105
VAL
151
A
ARG
152
n
106
ARG
152
A
LYS
153
n
107
LYS
153
A
SER
154
n
108
SER
154
A
LEU
155
n
109
LEU
155
A
SER
156
n
110
SER
156
A
ILE
157
n
111
ILE
157
A
LYS
158
n
112
LYS
158
A
PRO
159
n
113
PRO
159
A
ASN
160
n
114
ASN
160
A
ALA
161
n
115
ALA
161
A
ASP
162
n
116
ASP
162
A
GLY
163
n
117
GLY
163
A
SER
164
n
118
SER
164
A
GLY
165
n
119
GLY
165
A
TYR
166
n
120
TYR
166
A
PHE
167
n
121
PHE
167
A
ILE
168
n
122
ILE
168
A
SER
169
n
123
SER
169
A
LEU
170
n
124
LEU
170
A
SER
171
n
125
SER
171
A
VAL
172
n
126
VAL
172
A
VAL
173
n
127
VAL
173
A
ASN
174
n
128
ASN
174
A
ASN
175
n
129
ASN
175
A
ASN
176
n
130
ASN
176
A
LEU
177
n
131
LEU
177
A
LYS
178
n
132
LYS
178
A
THR
179
n
133
THR
179
A
ASN
180
n
134
ASN
180
A
ASP
181
n
135
ASP
181
A
ARG
182
n
136
ARG
182
A
PHE
183
n
137
PHE
183
A
THR
184
n
138
THR
184
A
VAL
185
n
139
VAL
185
A
PRO
186
n
140
PRO
186
A
VAL
187
n
141
VAL
187
A
THR
188
n
142
THR
188
A
THR
189
n
143
THR
189
A
ALA
190
n
144
ALA
190
A
GLU
191
n
145
GLU
191
A
PHE
192
n
146
PHE
192
A
ALA
193
n
147
ALA
193
A
VAL
194
n
148
VAL
194
A
MET
195
n
149
MET
195
A
ARG
196
n
150
ARG
196
A
THR
197
n
151
THR
197
A
ALA
198
n
152
ALA
198
A
PHE
199
n
153
PHE
199
A
SER
200
n
154
SER
200
A
PHE
201
n
155
PHE
201
A
ALA
202
n
156
ALA
202
A
LEU
203
n
157
LEU
203
A
PRO
204
n
158
PRO
204
A
HIS
205
n
159
HIS
205
A
ILE
206
n
160
ILE
206
A
MET
207
n
161
MET
207
A
GLY
208
n
162
GLY
208
A
TRP
209
n
163
TRP
209
A
ASP
210
n
164
ASP
210
A
ARG
211
n
165
ARG
211
A
PHE
212
n
166
PHE
212
A
THR
213
n
167
THR
213
A
ASN
214
n
168
ASN
214
A
ARG
215
n
169
ARG
215
A
n
170
216
A
n
171
217
A
n
172
218
A
n
173
219
A
n
174
220
A
n
175
221
A
n
176
222
A
n
177
223
A
n
178
224
A
DT
1
n
1
DT
1
B
DT
2
n
2
DT
2
B
DT
3
n
3
DT
3
B
DT
4
n
4
DT
4
B
DT
5
n
5
DT
5
B
DT
6
n
6
DT
6
B
DT
7
n
7
DT
7
B
DT
8
n
8
DT
8
B
DT
9
n
9
DT
9
B
software_defined_assembly
PISA
48
48-meric
author_and_software_defined_assembly
PISA
8
octameric
127190
-889
179220
16740
-142
34330
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
2_665
-x+1,-y+1,z
crystal symmetry operation
167.1640000000
167.1640000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
3_654
-x+1,y,-z-1
crystal symmetry operation
167.1640000000
0.0000000000
-167.1640000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_564
x,-y+1,-z-1
crystal symmetry operation
0.0000000000
167.1640000000
-167.1640000000
0.0000000000
0.0000000000
1.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
5_654
z+1,x,y-1
crystal symmetry operation
167.1640000000
0.0000000000
-167.1640000000
0.0000000000
0.0000000000
1.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
6_665
z+1,-x+1,-y
crystal symmetry operation
167.1640000000
167.1640000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
7_564
-z,-x+1,y-1
crystal symmetry operation
0.0000000000
167.1640000000
-167.1640000000
0.0000000000
0.0000000000
-1.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
8_555
-z,x,-y
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1.0000000000
0.0000000000
0.0000000000
9_564
y,z+1,x-1
crystal symmetry operation
0.0000000000
167.1640000000
-167.1640000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
-1.0000000000
0.0000000000
0.0000000000
10_665
-y+1,z+1,-x
crystal symmetry operation
167.1640000000
167.1640000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
-1.0000000000
0.0000000000
0.0000000000
11_555
y,-z,-x
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
1.0000000000
0.0000000000
0.0000000000
12_654
-y+1,-z,x-1
crystal symmetry operation
167.1640000000
0.0000000000
-167.1640000000
0.0000000000
1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
13_554
y,x,-z-1
crystal symmetry operation
0.0000000000
0.0000000000
-167.1640000000
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
14_664
-y+1,-x+1,-z-1
crystal symmetry operation
167.1640000000
167.1640000000
-167.1640000000
0.0000000000
1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
15_565
y,-x+1,z
crystal symmetry operation
0.0000000000
167.1640000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
16_655
-y+1,x,z
crystal symmetry operation
167.1640000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
-1.0000000000
0.0000000000
17_565
x,z+1,-y
crystal symmetry operation
0.0000000000
167.1640000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
1.0000000000
0.0000000000
18_664
-x+1,z+1,y-1
crystal symmetry operation
167.1640000000
167.1640000000
-167.1640000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
19_655
-x+1,-z,-y
crystal symmetry operation
167.1640000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
1.0000000000
0.0000000000
20_554
x,-z,y-1
crystal symmetry operation
0.0000000000
0.0000000000
-167.1640000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
21_655
z+1,y,-x
crystal symmetry operation
167.1640000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
-1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
22_664
z+1,-y+1,x-1
crystal symmetry operation
167.1640000000
167.1640000000
-167.1640000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
23_554
-z,y,x-1
crystal symmetry operation
0.0000000000
0.0000000000
-167.1640000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
24_565
-z,-y+1,-x
crystal symmetry operation
0.0000000000
167.1640000000
0.0000000000
A
N
VAL
63
A
N
VAL
17
A
O
LEU
70
A
O
LEU
24
A
N
ALA
69
A
N
ALA
23
A
O
TRP
100
A
O
TRP
54
A
N
LEU
97
A
N
LEU
51
A
O
PHE
116
A
O
PHE
70
A
N
ASN
80
A
N
ASN
34
A
O
LYS
88
A
O
LYS
42
A
N
HIS
139
A
N
HIS
93
A
O
LYS
153
A
O
LYS
107
A
N
LYS
158
A
N
LYS
112
A
O
PHE
167
A
O
PHE
121
A
N
TYR
166
A
N
TYR
120
A
O
VAL
187
A
O
VAL
141
1
A
MET
47
A
MET
1
1
Y
1
A
ALA
48
A
ALA
2
1
Y
1
A
ASP
49
A
ASP
3
1
Y
1
A
ALA
50
A
ALA
4
1
Y
1
A
GLY
51
A
GLY
5
1
Y
1
A
LYS
52
A
LYS
6
1
Y
1
A
ARG
53
A
ARG
7
1
Y
1
A
GLU
54
A
GLU
8
1
Y
1
A
PRO
216
A
PRO
170
1
Y
1
A
LEU
217
A
LEU
171
1
Y
1
A
GLU
218
A
GLU
172
1
Y
1
A
HIS
219
A
HIS
173
1
Y
1
A
HIS
220
A
HIS
174
1
Y
1
A
HIS
221
A
HIS
175
1
Y
1
A
HIS
222
A
HIS
176
1
Y
1
A
HIS
223
A
HIS
177
1
Y
1
A
HIS
224
A
HIS
178
1
Y
1
A
ASN
90
-103.21
-92.03
1
A
LEU
144
66.12
-6.88
53.56
1.0433
0.0000
0.0000
1.0433
-0.0000
1.0433
0.2618
0.2267
0.2295
2.200
32.171
755
10665
9840
7.67
92.11
0.35
RANDOM
1
Isotropic
THROUGHOUT
0.06
MOLECULAR REPLACEMENT
0.80
1.00
PDB ENTRY 1L3A
ML
FLAT BULK SOLVENT MODEL
43.592
0.330
2.200
32.171
36
1482
0
180
1266
0.008
1495
1.099
2056
16.539
561
0.060
225
0.004
236
0.4758
0.4689
2.3701
100
1252
65.00
0.3336
0.2909
2.6085
140
1877
97.00
0.3184
0.2644
2.9858
161
1908
99.00
0.2265
0.2141
3.7608
163
1955
99.00
0.2256
0.1852
32.1742
191
2093
99.00
40.49
2.20
50
3N1I
10693
10665
0
0
0.051
1
23.1
35.9
99.8
2.20
2.28
3.8
1028
0.56
9.9
98.7
refinement
PHENIX
(phenix.refine)
model building
PHENIX
refinement
CNS
data collection
CBASS
data reduction
HKL-2000
data scaling
HKL-2000
phasing
PHENIX
phasing
CNS
Crystal Structure of a StWhy2-ERE32 complex
1
N
N
2
N
N
3
N
N
3
N
N
Authors state that the biological unit is a tetramer protein plus a 32-mer DNA molecule, as indicated as pentamer in remark 350. Please refer to remark 999 for more details on the sequences specificity of this crystal structure.
A
ASP
109
A
ASP
63
HELX_P
A
ARG
113
A
ARG
67
5
1
5
A
SER
119
A
SER
73
HELX_P
A
SER
128
A
SER
82
1
2
10
A
THR
189
A
THR
143
HELX_P
A
MET
207
A
MET
161
1
3
19
A
GLY
208
A
GLY
162
HELX_P
A
PHE
212
A
PHE
166
5
4
5
DNA BINDING PROTEIN/DNA
Single-stranded DNA binding protein, Plant, Whirly, Protein-DNA complex, DNA BINDING PROTEIN-DNA complex
3N1I
PDB
1
1
3N1I
MADAGKREGRVFAPYSVFKGKAALSAEPRLPTFNRLDSGGVKLNRRGVIMLTFWPSVGERKYDWEKRQLFALSATEVGSL
ISMGTRDSSEFFHDPSMLSSNAGQVRKSLSIKPNADGSGYFISLSVVNNNLKTNDRFTVPVTTAEFAVMRTAFSFALPHI
MGWDRFTNRPLEHHHHHH
3N1I
PDB
2
1
3N1I
TTTTTTTTT
47
224
3N1I
47
224
3N1I
A
1
1
178
1
9
3N1I
1
9
3N1I
B
2
1
9
4
2
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TYR
61
A
TYR
15
A
PHE
64
A
PHE
18
A
ALA
68
A
ALA
22
A
ARG
75
A
ARG
29
A
VAL
94
A
VAL
48
A
PRO
101
A
PRO
55
A
GLN
114
A
GLN
68
A
LEU
118
A
LEU
72
A
PHE
79
A
PHE
33
A
ARG
81
A
ARG
35
A
VAL
87
A
VAL
41
A
LEU
89
A
LEU
43
A
SER
135
A
SER
89
A
HIS
139
A
HIS
93
A
VAL
151
A
VAL
105
A
PRO
159
A
PRO
113
A
GLY
165
A
GLY
119
A
ASN
174
A
ASN
128
A
THR
179
A
THR
133
A
THR
188
A
THR
142
209
F 4 3 2