0.024739
0.014283
0.000000
0.000000
0.028566
0.000000
0.000000
0.000000
0.008465
0.00000
0.00000
0.00000
Shimizu, N.
Kamikubo, H.
Yamazaki, Y.
Imamoto, Y.
Kataoka, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
40.422
40.422
118.131
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
C9 H8 O3
164.158
4'-HYDROXYCINNAMIC ACID
PARA-COUMARIC ACID
non-polymer
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
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
C
N
138
N
O
N
139
N
O
N
140
N
C
N
141
N
C
Y
142
N
C
Y
143
N
C
Y
144
N
C
Y
145
N
C
Y
146
N
C
Y
147
N
C
N
148
N
O
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
N
N
158
S
C
N
159
N
C
N
160
N
O
N
161
N
C
Y
162
N
C
Y
163
N
N
Y
164
N
C
Y
165
N
C
Y
166
N
N
N
167
N
O
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
O
N
179
N
H
N
180
N
H
N
181
N
N
N
182
S
C
N
183
N
C
N
184
N
O
N
185
S
C
N
186
N
C
N
187
N
C
N
188
N
C
N
189
N
O
N
190
N
H
N
191
N
H
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
N
N
204
S
C
N
205
N
C
N
206
N
O
N
207
N
C
N
208
N
C
N
209
N
C
N
210
N
C
N
211
N
O
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
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
N
N
226
S
C
N
227
N
C
N
228
N
O
N
229
N
C
N
230
N
C
N
231
N
C
N
232
N
C
N
233
N
N
N
234
N
O
N
235
N
H
N
236
N
H
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
N
N
251
S
C
N
252
N
C
N
253
N
O
N
254
N
C
N
255
N
C
N
256
N
S
N
257
N
C
N
258
N
O
N
259
N
H
N
260
N
H
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
N
N
271
S
C
N
272
N
C
N
273
N
O
N
274
N
C
Y
275
N
C
Y
276
N
C
Y
277
N
C
Y
278
N
C
Y
279
N
C
Y
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
H
N
292
N
H
N
293
N
N
N
294
S
C
N
295
N
C
N
296
N
O
N
297
N
C
N
298
N
C
N
299
N
C
N
300
N
O
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
N
N
311
S
C
N
312
N
C
N
313
N
O
N
314
N
C
N
315
N
O
N
316
N
O
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
N
N
325
S
C
N
326
N
C
N
327
N
O
N
328
R
C
N
329
N
O
N
330
N
C
N
331
N
O
N
332
N
H
N
333
N
H
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
N
N
342
S
C
N
343
N
C
N
344
N
O
N
345
N
C
Y
346
N
C
Y
347
N
C
Y
348
N
C
Y
349
N
N
Y
350
N
C
Y
351
N
C
Y
352
N
C
Y
353
N
C
Y
354
N
C
N
355
N
O
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
365
N
H
N
366
N
H
N
367
N
H
N
368
N
N
N
369
S
C
N
370
N
C
N
371
N
O
N
372
N
C
Y
373
N
C
Y
374
N
C
Y
375
N
C
Y
376
N
C
Y
377
N
C
Y
378
N
C
N
379
N
O
N
380
N
O
N
381
N
H
N
382
N
H
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
N
N
393
S
C
N
394
N
C
N
395
N
O
N
396
N
C
N
397
N
C
N
398
N
C
N
399
N
O
N
400
N
H
N
401
N
H
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
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
doub
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
E
doub
N
134
N
sing
N
135
N
sing
N
136
N
sing
Y
137
N
doub
Y
138
N
sing
Y
139
N
sing
N
140
N
sing
Y
141
N
doub
N
142
N
sing
Y
143
N
sing
N
144
N
sing
Y
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
doub
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
Y
160
N
sing
Y
161
N
doub
Y
162
N
doub
N
163
N
sing
Y
164
N
sing
N
165
N
sing
Y
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
doub
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
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
doub
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
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
doub
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
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
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
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
doub
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
Y
268
N
doub
Y
269
N
sing
Y
270
N
sing
N
271
N
sing
Y
272
N
doub
N
273
N
sing
Y
274
N
doub
N
275
N
sing
Y
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
doub
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
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
doub
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
sing
N
316
N
doub
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
doub
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
Y
337
N
doub
Y
338
N
sing
Y
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
sing
Y
346
N
doub
N
347
N
sing
Y
348
N
doub
N
349
N
sing
Y
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
Y
365
N
doub
Y
366
N
sing
Y
367
N
sing
N
368
N
sing
Y
369
N
doub
N
370
N
sing
Y
371
N
doub
N
372
N
sing
Y
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
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
doub
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
US
Biochemistry
BICHAW
0033
0006-2960
45
3542
3547
10.1021/bi051430a
16533035
The Crystal Structure of the R52Q Mutant Demonstrates a Role for R52 in Chromophore pK(a) Regulation in Photoactive Yellow Protein
2006
10.2210/pdb2d01/pdb
pdb_00002d01
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
bending magnet
CCD
2004-03-26
ADSC QUANTUM 4
fixed-exit double crystal monochromator
SINGLE WAVELENGTH
M
x-ray
1
1.000
1.0
BL40B2
SPring-8
1.000
SYNCHROTRON
SPRING-8 BEAMLINE BL40B2
13888.575
Photoactive yellow protein
1
man
polymer
164.158
4'-HYDROXYCINNAMIC ACID
1
syn
non-polymer
18.015
water
210
nat
water
Photoreceptor, PYP
no
no
MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK
EGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV
MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK
EGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV
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
Halorhodospira
Escherichia
Escherichia coli
sample
PYP
1053
Halorhodospira halophila
469008
Escherichia coli BL21(DE3)
BL21DE3
PLASMID
PET
1
2.0
38.9
VAPOR DIFFUSION
6.5
40% PEG2000, 100mM sodium citrate, pH 6.5, VAPOR DIFFUSION, temperature 293K
293
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2006-04-04
1
1
2008-04-30
1
2
2011-07-13
1
3
2023-10-25
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
another crystal form of PYP
PYP(R52Q), P65 Form
PDBJ
Y
PDBJ
2005-07-21
REL
REL
HC4
4'-HYDROXYCINNAMIC ACID
HOH
water
2PHY
PDB
experimental model
HC4
169
2
HC4
HC4
169
A
HOH
1
3
HOH
HOH
170
A
HOH
2
3
HOH
HOH
171
A
HOH
3
3
HOH
HOH
172
A
HOH
4
3
HOH
HOH
173
A
HOH
5
3
HOH
HOH
174
A
HOH
6
3
HOH
HOH
175
A
HOH
7
3
HOH
HOH
176
A
HOH
8
3
HOH
HOH
177
A
HOH
9
3
HOH
HOH
178
A
HOH
10
3
HOH
HOH
179
A
HOH
11
3
HOH
HOH
180
A
HOH
12
3
HOH
HOH
181
A
HOH
13
3
HOH
HOH
182
A
HOH
14
3
HOH
HOH
183
A
HOH
15
3
HOH
HOH
184
A
HOH
16
3
HOH
HOH
185
A
HOH
17
3
HOH
HOH
186
A
HOH
18
3
HOH
HOH
187
A
HOH
19
3
HOH
HOH
188
A
HOH
20
3
HOH
HOH
189
A
HOH
21
3
HOH
HOH
190
A
HOH
22
3
HOH
HOH
191
A
HOH
23
3
HOH
HOH
192
A
HOH
24
3
HOH
HOH
193
A
HOH
25
3
HOH
HOH
194
A
HOH
26
3
HOH
HOH
195
A
HOH
27
3
HOH
HOH
196
A
HOH
28
3
HOH
HOH
197
A
HOH
29
3
HOH
HOH
198
A
HOH
30
3
HOH
HOH
199
A
HOH
31
3
HOH
HOH
200
A
HOH
32
3
HOH
HOH
201
A
HOH
33
3
HOH
HOH
202
A
HOH
34
3
HOH
HOH
203
A
HOH
35
3
HOH
HOH
204
A
HOH
36
3
HOH
HOH
205
A
HOH
37
3
HOH
HOH
206
A
HOH
38
3
HOH
HOH
207
A
HOH
39
3
HOH
HOH
208
A
HOH
40
3
HOH
HOH
209
A
HOH
41
3
HOH
HOH
210
A
HOH
42
3
HOH
HOH
211
A
HOH
43
3
HOH
HOH
212
A
HOH
44
3
HOH
HOH
213
A
HOH
45
3
HOH
HOH
214
A
HOH
46
3
HOH
HOH
215
A
HOH
47
3
HOH
HOH
216
A
HOH
48
3
HOH
HOH
217
A
HOH
49
3
HOH
HOH
218
A
HOH
50
3
HOH
HOH
219
A
HOH
51
3
HOH
HOH
220
A
HOH
52
3
HOH
HOH
221
A
HOH
53
3
HOH
HOH
222
A
HOH
54
3
HOH
HOH
223
A
HOH
55
3
HOH
HOH
224
A
HOH
56
3
HOH
HOH
225
A
HOH
57
3
HOH
HOH
226
A
HOH
58
3
HOH
HOH
227
A
HOH
59
3
HOH
HOH
228
A
HOH
60
3
HOH
HOH
229
A
HOH
61
3
HOH
HOH
230
A
HOH
62
3
HOH
HOH
231
A
HOH
63
3
HOH
HOH
232
A
HOH
64
3
HOH
HOH
233
A
HOH
65
3
HOH
HOH
234
A
HOH
66
3
HOH
HOH
235
A
HOH
67
3
HOH
HOH
236
A
HOH
68
3
HOH
HOH
237
A
HOH
69
3
HOH
HOH
238
A
HOH
70
3
HOH
HOH
239
A
HOH
71
3
HOH
HOH
240
A
HOH
72
3
HOH
HOH
241
A
HOH
73
3
HOH
HOH
242
A
HOH
74
3
HOH
HOH
243
A
HOH
75
3
HOH
HOH
244
A
HOH
76
3
HOH
HOH
245
A
HOH
77
3
HOH
HOH
246
A
HOH
78
3
HOH
HOH
247
A
HOH
79
3
HOH
HOH
248
A
HOH
80
3
HOH
HOH
249
A
HOH
81
3
HOH
HOH
250
A
HOH
82
3
HOH
HOH
251
A
HOH
83
3
HOH
HOH
252
A
HOH
84
3
HOH
HOH
253
A
HOH
85
3
HOH
HOH
254
A
HOH
86
3
HOH
HOH
255
A
HOH
87
3
HOH
HOH
256
A
HOH
88
3
HOH
HOH
257
A
HOH
89
3
HOH
HOH
258
A
HOH
90
3
HOH
HOH
259
A
HOH
91
3
HOH
HOH
260
A
HOH
92
3
HOH
HOH
261
A
HOH
93
3
HOH
HOH
262
A
HOH
94
3
HOH
HOH
263
A
HOH
95
3
HOH
HOH
264
A
HOH
96
3
HOH
HOH
265
A
HOH
97
3
HOH
HOH
266
A
HOH
98
3
HOH
HOH
267
A
HOH
99
3
HOH
HOH
268
A
HOH
100
3
HOH
HOH
269
A
HOH
101
3
HOH
HOH
270
A
HOH
102
3
HOH
HOH
271
A
HOH
103
3
HOH
HOH
272
A
HOH
104
3
HOH
HOH
273
A
HOH
105
3
HOH
HOH
274
A
HOH
106
3
HOH
HOH
275
A
HOH
107
3
HOH
HOH
276
A
HOH
108
3
HOH
HOH
277
A
HOH
109
3
HOH
HOH
278
A
HOH
110
3
HOH
HOH
279
A
HOH
111
3
HOH
HOH
280
A
HOH
112
3
HOH
HOH
281
A
HOH
113
3
HOH
HOH
282
A
HOH
114
3
HOH
HOH
283
A
HOH
115
3
HOH
HOH
284
A
HOH
116
3
HOH
HOH
285
A
HOH
117
3
HOH
HOH
286
A
HOH
118
3
HOH
HOH
287
A
HOH
119
3
HOH
HOH
288
A
HOH
120
3
HOH
HOH
289
A
HOH
121
3
HOH
HOH
290
A
HOH
122
3
HOH
HOH
291
A
HOH
123
3
HOH
HOH
292
A
HOH
124
3
HOH
HOH
293
A
HOH
125
3
HOH
HOH
294
A
HOH
126
3
HOH
HOH
295
A
HOH
127
3
HOH
HOH
296
A
HOH
128
3
HOH
HOH
297
A
HOH
129
3
HOH
HOH
298
A
HOH
130
3
HOH
HOH
299
A
HOH
131
3
HOH
HOH
300
A
HOH
132
3
HOH
HOH
301
A
HOH
133
3
HOH
HOH
302
A
HOH
134
3
HOH
HOH
303
A
HOH
135
3
HOH
HOH
304
A
HOH
136
3
HOH
HOH
305
A
HOH
137
3
HOH
HOH
306
A
HOH
138
3
HOH
HOH
307
A
HOH
139
3
HOH
HOH
308
A
HOH
140
3
HOH
HOH
309
A
HOH
141
3
HOH
HOH
310
A
HOH
142
3
HOH
HOH
311
A
HOH
143
3
HOH
HOH
312
A
HOH
144
3
HOH
HOH
313
A
HOH
145
3
HOH
HOH
314
A
HOH
146
3
HOH
HOH
315
A
HOH
147
3
HOH
HOH
316
A
HOH
148
3
HOH
HOH
317
A
HOH
149
3
HOH
HOH
318
A
HOH
150
3
HOH
HOH
319
A
HOH
151
3
HOH
HOH
320
A
HOH
152
3
HOH
HOH
321
A
HOH
153
3
HOH
HOH
322
A
HOH
154
3
HOH
HOH
323
A
HOH
155
3
HOH
HOH
324
A
HOH
156
3
HOH
HOH
325
A
HOH
157
3
HOH
HOH
326
A
HOH
158
3
HOH
HOH
327
A
HOH
159
3
HOH
HOH
328
A
HOH
160
3
HOH
HOH
329
A
HOH
161
3
HOH
HOH
330
A
HOH
162
3
HOH
HOH
331
A
HOH
163
3
HOH
HOH
332
A
HOH
164
3
HOH
HOH
333
A
HOH
165
3
HOH
HOH
334
A
HOH
166
3
HOH
HOH
335
A
HOH
167
3
HOH
HOH
336
A
HOH
168
3
HOH
HOH
337
A
HOH
169
3
HOH
HOH
338
A
HOH
170
3
HOH
HOH
339
A
HOH
171
3
HOH
HOH
340
A
HOH
172
3
HOH
HOH
341
A
HOH
173
3
HOH
HOH
342
A
HOH
174
3
HOH
HOH
343
A
HOH
175
3
HOH
HOH
344
A
HOH
176
3
HOH
HOH
345
A
HOH
177
3
HOH
HOH
346
A
HOH
178
3
HOH
HOH
347
A
HOH
179
3
HOH
HOH
348
A
HOH
180
3
HOH
HOH
349
A
HOH
181
3
HOH
HOH
350
A
HOH
182
3
HOH
HOH
351
A
HOH
183
3
HOH
HOH
352
A
HOH
184
3
HOH
HOH
353
A
HOH
185
3
HOH
HOH
354
A
HOH
186
3
HOH
HOH
355
A
HOH
187
3
HOH
HOH
356
A
HOH
188
3
HOH
HOH
357
A
HOH
189
3
HOH
HOH
358
A
HOH
190
3
HOH
HOH
359
A
HOH
191
3
HOH
HOH
360
A
HOH
192
3
HOH
HOH
361
A
HOH
193
3
HOH
HOH
362
A
HOH
194
3
HOH
HOH
363
A
HOH
195
3
HOH
HOH
364
A
HOH
196
3
HOH
HOH
365
A
HOH
197
3
HOH
HOH
366
A
HOH
198
3
HOH
HOH
367
A
HOH
199
3
HOH
HOH
368
A
HOH
200
3
HOH
HOH
369
A
HOH
201
3
HOH
HOH
370
A
HOH
202
3
HOH
HOH
371
A
HOH
203
3
HOH
HOH
372
A
HOH
204
3
HOH
HOH
373
A
HOH
205
3
HOH
HOH
374
A
HOH
206
3
HOH
HOH
375
A
HOH
207
3
HOH
HOH
376
A
HOH
208
3
HOH
HOH
377
A
HOH
209
3
HOH
HOH
378
A
HOH
210
3
HOH
HOH
379
A
n
1
1
A
GLU
2
n
2
GLU
2
A
HIS
3
n
3
HIS
3
A
VAL
4
n
4
VAL
4
A
ALA
5
n
5
ALA
5
A
PHE
6
n
6
PHE
6
A
GLY
7
n
7
GLY
7
A
SER
8
n
8
SER
8
A
GLU
9
n
9
GLU
9
A
ASP
10
n
10
ASP
10
A
ILE
11
n
11
ILE
11
A
GLU
12
n
12
GLU
12
A
ASN
13
n
13
ASN
13
A
THR
14
n
14
THR
14
A
LEU
15
n
15
LEU
15
A
ALA
16
n
16
ALA
16
A
LYS
17
n
17
LYS
17
A
MET
18
n
18
MET
18
A
ASP
19
n
19
ASP
19
A
ASP
20
n
20
ASP
20
A
GLY
21
n
21
GLY
21
A
GLN
22
n
22
GLN
22
A
LEU
23
n
23
LEU
23
A
ASP
24
n
24
ASP
24
A
GLY
25
n
25
GLY
25
A
LEU
26
n
26
LEU
26
A
ALA
27
n
27
ALA
27
A
PHE
28
n
28
PHE
28
A
GLY
29
n
29
GLY
29
A
ALA
30
n
30
ALA
30
A
ILE
31
n
31
ILE
31
A
GLN
32
n
32
GLN
32
A
LEU
33
n
33
LEU
33
A
ASP
34
n
34
ASP
34
A
GLY
35
n
35
GLY
35
A
ASP
36
n
36
ASP
36
A
GLY
37
n
37
GLY
37
A
ASN
38
n
38
ASN
38
A
ILE
39
n
39
ILE
39
A
LEU
40
n
40
LEU
40
A
GLN
41
n
41
GLN
41
A
TYR
42
n
42
TYR
42
A
ASN
43
n
43
ASN
43
A
ALA
44
n
44
ALA
44
A
ALA
45
n
45
ALA
45
A
GLU
46
n
46
GLU
46
A
GLY
47
n
47
GLY
47
A
ASP
48
n
48
ASP
48
A
ILE
49
n
49
ILE
49
A
THR
50
n
50
THR
50
A
GLY
51
n
51
GLY
51
A
ARG
52
n
52
ARG
52
A
ASP
53
n
53
ASP
53
A
PRO
54
n
54
PRO
54
A
LYS
55
n
55
LYS
55
A
GLN
56
n
56
GLN
56
A
VAL
57
n
57
VAL
57
A
ILE
58
n
58
ILE
58
A
GLY
59
n
59
GLY
59
A
LYS
60
n
60
LYS
60
A
ASN
61
n
61
ASN
61
A
PHE
62
n
62
PHE
62
A
PHE
63
n
63
PHE
63
A
LYS
64
n
64
LYS
64
A
ASP
65
n
65
ASP
65
A
VAL
66
n
66
VAL
66
A
ALA
67
n
67
ALA
67
A
PRO
68
n
68
PRO
68
A
CYS
69
n
69
CYS
69
A
THR
70
n
70
THR
70
A
ASP
71
n
71
ASP
71
A
SER
72
n
72
SER
72
A
PRO
73
n
73
PRO
73
A
GLU
74
n
74
GLU
74
A
PHE
75
n
75
PHE
75
A
TYR
76
n
76
TYR
76
A
GLY
77
n
77
GLY
77
A
LYS
78
n
78
LYS
78
A
PHE
79
n
79
PHE
79
A
LYS
80
n
80
LYS
80
A
GLU
81
n
81
GLU
81
A
GLY
82
n
82
GLY
82
A
VAL
83
n
83
VAL
83
A
ALA
84
n
84
ALA
84
A
SER
85
n
85
SER
85
A
GLY
86
n
86
GLY
86
A
ASN
87
n
87
ASN
87
A
LEU
88
n
88
LEU
88
A
ASN
89
n
89
ASN
89
A
THR
90
n
90
THR
90
A
MET
91
n
91
MET
91
A
PHE
92
n
92
PHE
92
A
GLU
93
n
93
GLU
93
A
TYR
94
n
94
TYR
94
A
THR
95
n
95
THR
95
A
PHE
96
n
96
PHE
96
A
ASP
97
n
97
ASP
97
A
TYR
98
n
98
TYR
98
A
GLN
99
n
99
GLN
99
A
MET
100
n
100
MET
100
A
THR
101
n
101
THR
101
A
PRO
102
n
102
PRO
102
A
THR
103
n
103
THR
103
A
LYS
104
n
104
LYS
104
A
VAL
105
n
105
VAL
105
A
LYS
106
n
106
LYS
106
A
VAL
107
n
107
VAL
107
A
HIS
108
n
108
HIS
108
A
MET
109
n
109
MET
109
A
LYS
110
n
110
LYS
110
A
LYS
111
n
111
LYS
111
A
ALA
112
n
112
ALA
112
A
LEU
113
n
113
LEU
113
A
SER
114
n
114
SER
114
A
GLY
115
n
115
GLY
115
A
ASP
116
n
116
ASP
116
A
SER
117
n
117
SER
117
A
TYR
118
n
118
TYR
118
A
TRP
119
n
119
TRP
119
A
VAL
120
n
120
VAL
120
A
PHE
121
n
121
PHE
121
A
VAL
122
n
122
VAL
122
A
LYS
123
n
123
LYS
123
A
ARG
124
n
124
ARG
124
A
VAL
125
n
125
VAL
125
A
author_defined_assembly
1
monomeric
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
O
LEU
40
A
O
LEU
40
A
N
GLN
32
A
N
GLN
32
A
N
LEU
33
A
N
LEU
33
A
O
TYR
118
A
O
TYR
118
A
O
TRP
119
A
O
TRP
119
A
N
LYS
110
A
N
LYS
110
A
O
VAL
107
A
O
VAL
107
A
N
PHE
92
A
N
PHE
92
1
A
MET
1
A
MET
1
1
Y
1
A
A
OD2
O
ASP
HOH
19
352
2.07
B
1
A
A
OD1
O
ASP
HOH
19
305
2.19
B
1
A
PHE
75
-129.54
-75.85
1
A
ASN
89
-168.55
92.36
1
A
ASP
97
-146.98
14.44
16.989
0.53
0.27
0.00
0.53
0.00
-0.80
0.974
0.962
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.18915
0.15209
0.15397
1.34
20.00
1244
23170
5.1
99.91
1.817
0.035
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.067
0.060
0.80
0.80
1.20
2PHY
MAXIMUM LIKELIHOOD
MASK
1.34
20.00
210
1246
11
0
1025
0.012
0.022
1057
1.487
1.972
1412
6.074
5.000
123
36.474
25.818
55
15.769
15.000
208
12.980
15.000
3
0.102
0.200
142
0.008
0.020
804
0.257
0.200
535
0.316
0.200
735
0.185
0.200
178
0.210
0.200
39
0.164
0.200
31
1.596
1.500
631
2.289
2.000
993
2.857
3.000
484
3.615
4.500
419
2.094
3.000
1115
5.360
3.000
210
4.264
3.000
1036
1706
20
1.34
20.09
2D01
23170
0.053
1
14.2
11.1
99.8
0.303
1.34
1.39
9.09
11.0
99.8
refinement
REFMAC
5.2.0005
data reduction
HKL-2000
data scaling
SCALEPACK
phasing
AMoRE
Wild Type Photoactive Yellow Protein, P65 Form
1
N
N
2
N
N
3
N
N
A
ASP
10
A
ASP
10
HELX_P
A
LYS
17
A
LYS
17
1
1
8
A
ASP
19
A
ASP
19
HELX_P
A
GLY
25
A
GLY
25
1
2
7
A
ASN
43
A
ASN
43
HELX_P
A
GLY
51
A
GLY
51
1
3
9
A
ASP
53
A
ASP
53
HELX_P
A
ILE
58
A
ILE
58
1
4
6
A
ALA
67
A
ALA
67
HELX_P
A
ASP
71
A
ASP
71
5
5
5
A
PHE
75
A
PHE
75
HELX_P
A
GLY
86
A
GLY
86
1
6
12
covale
1.772
one
A
CYS
69
A
SG
CYS
69
1_555
A
HC4
169
B
C1
HC4
1_555
SIGNALING PROTEIN
PAS, LOV, GAF-DOMAINS, PHOTORECEPTOR, SIGNALING PROTEIN
PYP_ECTHA
UNP
1
1
P16113
1
125
2D01
1
125
P16113
A
1
1
125
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ILE
39
A
ILE
39
A
TYR
42
A
TYR
42
A
GLY
29
A
GLY
29
A
LEU
33
A
LEU
33
A
TYR
118
A
TYR
118
A
ARG
124
A
ARG
124
A
THR
103
A
THR
103
A
LYS
111
A
LYS
111
A
ASN
89
A
ASN
89
A
PHE
96
A
PHE
96
BINDING SITE FOR RESIDUE HC4 A 169
A
HC4
169
Software
11
A
ILE
31
A
ILE
31
11
1_555
A
TYR
42
A
TYR
42
11
1_555
A
GLU
46
A
GLU
46
11
1_555
A
THR
50
A
THR
50
11
1_555
A
ARG
52
A
ARG
52
11
1_555
A
VAL
66
A
VAL
66
11
1_555
A
ALA
67
A
ALA
67
11
1_555
A
PRO
68
A
PRO
68
11
1_555
A
CYS
69
A
CYS
69
11
1_555
A
PHE
96
A
PHE
96
11
1_555
A
TYR
98
A
TYR
98
11
1_555
170
P 65