0.017658
0.010195
0.000000
0.000000
0.020390
0.000000
0.000000
0.000000
0.007233
0.00000
0.00000
0.00000
Gogos, A.
Mu, H.
Bahna, F.
Gomez, C.A.
Shapiro, L.
0000-0002-2487-9713
Burley, S.K.
New York SGX Research Center for Structural Genomics (NYSGXRC)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
56.630
56.630
138.257
C11 H24 O6
252.305
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
non-polymer
C2 H4 O2
60.052
ACETIC ACID
non-polymer
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
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
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
C
N
2
N
C
N
3
N
O
N
4
N
O
N
5
N
C
N
6
N
C
N
7
N
C
N
8
N
O
N
9
N
C
N
10
N
C
N
11
N
O
N
12
N
C
N
13
N
C
N
14
N
O
N
15
N
C
N
16
N
C
N
17
N
O
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
H
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
H
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
H
N
42
N
C
N
43
N
O
N
44
N
O
N
45
N
C
N
46
N
H
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
N
N
51
S
C
N
52
N
C
N
53
N
O
N
54
N
C
N
55
N
O
N
56
N
H
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
N
N
64
S
C
N
65
N
C
N
66
N
O
N
67
N
C
N
68
N
C
N
69
N
C
N
70
N
N
N
71
N
C
N
72
N
N
N
73
N
N
N
74
N
O
N
75
N
H
N
76
N
H
N
77
N
H
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
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
N
N
91
S
C
N
92
N
C
N
93
N
O
N
94
N
C
N
95
N
C
N
96
N
O
N
97
N
N
N
98
N
O
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
N
N
108
S
C
N
109
N
C
N
110
N
O
N
111
N
C
N
112
N
C
N
113
N
O
N
114
N
O
N
115
N
O
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
N
N
132
N
O
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
N
N
144
S
C
N
145
N
C
N
146
N
O
N
147
N
C
N
148
N
C
N
149
N
C
N
150
N
O
N
151
N
O
N
152
N
O
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
N
N
163
N
C
N
164
N
C
N
165
N
O
N
166
N
O
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
N
N
173
S
C
N
174
N
C
N
175
N
O
N
176
N
C
Y
177
N
C
Y
178
N
N
Y
179
N
C
Y
180
N
C
Y
181
N
N
N
182
N
O
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
O
N
194
N
H
N
195
N
H
N
196
N
N
N
197
S
C
N
198
N
C
N
199
N
O
N
200
S
C
N
201
N
C
N
202
N
C
N
203
N
C
N
204
N
O
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
H
N
218
N
N
N
219
S
C
N
220
N
C
N
221
N
O
N
222
N
C
N
223
N
C
N
224
N
C
N
225
N
C
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
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
C
N
247
N
C
N
248
N
N
N
249
N
O
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
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
N
N
266
S
C
N
267
N
C
N
268
N
O
N
269
N
C
N
270
N
C
N
271
N
S
N
272
N
C
N
273
N
O
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
H
N
284
N
H
N
285
N
N
N
286
S
C
N
287
N
C
N
288
N
O
N
289
N
C
Y
290
N
C
Y
291
N
C
Y
292
N
C
Y
293
N
C
Y
294
N
C
Y
295
N
C
N
296
N
O
N
297
N
H
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
H
N
306
N
H
N
307
N
H
N
308
N
N
N
309
S
C
N
310
N
C
N
311
N
O
N
312
N
C
N
313
N
C
N
314
N
C
N
315
N
O
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
H
N
323
N
H
N
324
N
H
N
325
N
N
N
326
S
C
N
327
N
C
N
328
N
O
N
329
N
C
N
330
N
O
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
N
N
340
S
C
N
341
N
C
N
342
N
O
N
343
R
C
N
344
N
O
N
345
N
C
N
346
N
O
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
N
N
357
S
C
N
358
N
C
N
359
N
O
N
360
N
C
Y
361
N
C
Y
362
N
C
Y
363
N
C
Y
364
N
C
Y
365
N
C
Y
366
N
C
N
367
N
O
N
368
N
O
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
H
N
380
N
N
N
381
S
C
N
382
N
C
N
383
N
O
N
384
N
C
N
385
N
C
N
386
N
C
N
387
N
O
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
H
N
397
N
H
N
398
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
sing
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
sing
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
sing
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
doub
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
doub
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
sing
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
doub
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
doub
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
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
sing
N
122
N
sing
N
123
N
doub
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
doub
N
132
N
sing
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
sing
N
141
N
sing
N
142
N
doub
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
sing
N
160
N
doub
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
doub
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
Y
174
N
sing
Y
175
N
doub
Y
176
N
doub
N
177
N
sing
Y
178
N
sing
N
179
N
sing
Y
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
doub
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
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
doub
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
sing
N
234
N
doub
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
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
doub
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
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
doub
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
Y
282
N
doub
Y
283
N
sing
Y
284
N
sing
N
285
N
sing
Y
286
N
doub
N
287
N
sing
Y
288
N
doub
N
289
N
sing
Y
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
doub
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
sing
N
316
N
sing
N
317
N
doub
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
doub
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
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
doub
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
Y
351
N
doub
Y
352
N
sing
Y
353
N
sing
N
354
N
sing
Y
355
N
doub
N
356
N
sing
Y
357
N
doub
N
358
N
sing
Y
359
N
sing
N
360
N
sing
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
doub
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
sing
N
380
N
sing
N
381
N
sing
US
PROTEINS: STRUCT.,FUNCT.,GENET.
PSFGEY
0867
0887-3585
53
320
322
10.1002/prot.10457
14517982
Crystal structure of YdcE protein from Bacillus subtilis
2003
10.2210/pdb1ne8/pdb
pdb_00001ne8
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
2002-09-01
ADSC QUANTUM 4
MAD
M
x-ray
1
0.9790
1.0
0.97938
1.0
0.97163
1.0
X9A
NSLS
0.9790, 0.97938, 0.97163
SYNCHROTRON
NSLS BEAMLINE X9A
13062.981
conserved hypothetical protein YDCE
1
man
polymer
252.305
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2
syn
non-polymer
60.052
ACETIC ACID
2
syn
non-polymer
18.015
water
100
nat
water
no
no
SLIVKRGDVYFADLSPVVGSEQGGVRPVLVIQNDIGNRFSPTAIVAAITAQIQKAKLPTHVEIDAKRYGFERDSVILLEQ
IRTIDKQRLTDKITHLDDEMMDKVDEALQISLALIDF
SLIVKRGDVYFADLSPVVGSEQGGVRPVLVIQNDIGNRFSPTAIVAAITAQIQKAKLPTHVEIDAKRYGFERDSVILLEQ
IRTIDKQRLTDKITHLDDEMMDKVDEALQISLALIDF
A
NYSGXRC-T503
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
Bacillus
Escherichia
Escherichia coli
sample
ydcE
1423
Bacillus subtilis
511693
Escherichia coli BL21
BL21
plasmid
pSMT3
1
2.45
49.77
VAPOR DIFFUSION, HANGING DROP
4.6
12% PEG 4,000 0.1M Sodium Acetate pH 4.6, 0.2M Ammonium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
New York SGX Research Center for Structural Genomics
NYSGXRC
PSI, Protein Structure Initiative
software
audit_author
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
database_2
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Database references
Derived calculations
Structure summary
Data collection
Database references
1
0
2003-01-14
1
1
2008-04-28
1
2
2011-07-13
1
3
2017-10-11
1
4
2021-02-03
1
5
2024-02-14
_audit_author.identifier_ORCID
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
Y
RCSB
Y
RCSB
2002-12-10
REL
REL
1PG
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
ACY
ACETIC ACID
HOH
water
1PG
501
2
1PG
1PG
501
A
1PG
503
2
1PG
1PG
503
A
ACY
502
3
ACY
ACY
502
A
ACY
504
3
ACY
ACY
504
A
HOH
1
4
HOH
HOH
505
A
HOH
2
4
HOH
HOH
506
A
HOH
3
4
HOH
HOH
507
A
HOH
4
4
HOH
HOH
508
A
HOH
5
4
HOH
HOH
509
A
HOH
6
4
HOH
HOH
510
A
HOH
7
4
HOH
HOH
511
A
HOH
8
4
HOH
HOH
512
A
HOH
9
4
HOH
HOH
513
A
HOH
10
4
HOH
HOH
514
A
HOH
11
4
HOH
HOH
515
A
HOH
12
4
HOH
HOH
516
A
HOH
13
4
HOH
HOH
517
A
HOH
14
4
HOH
HOH
518
A
HOH
15
4
HOH
HOH
519
A
HOH
16
4
HOH
HOH
520
A
HOH
17
4
HOH
HOH
521
A
HOH
18
4
HOH
HOH
522
A
HOH
19
4
HOH
HOH
523
A
HOH
20
4
HOH
HOH
524
A
HOH
21
4
HOH
HOH
525
A
HOH
22
4
HOH
HOH
526
A
HOH
23
4
HOH
HOH
527
A
HOH
24
4
HOH
HOH
528
A
HOH
25
4
HOH
HOH
529
A
HOH
26
4
HOH
HOH
530
A
HOH
27
4
HOH
HOH
531
A
HOH
28
4
HOH
HOH
532
A
HOH
29
4
HOH
HOH
533
A
HOH
30
4
HOH
HOH
534
A
HOH
31
4
HOH
HOH
535
A
HOH
32
4
HOH
HOH
536
A
HOH
33
4
HOH
HOH
537
A
HOH
34
4
HOH
HOH
538
A
HOH
35
4
HOH
HOH
539
A
HOH
36
4
HOH
HOH
540
A
HOH
37
4
HOH
HOH
541
A
HOH
38
4
HOH
HOH
542
A
HOH
39
4
HOH
HOH
543
A
HOH
40
4
HOH
HOH
544
A
HOH
41
4
HOH
HOH
545
A
HOH
42
4
HOH
HOH
546
A
HOH
43
4
HOH
HOH
547
A
HOH
44
4
HOH
HOH
548
A
HOH
45
4
HOH
HOH
549
A
HOH
46
4
HOH
HOH
550
A
HOH
47
4
HOH
HOH
551
A
HOH
48
4
HOH
HOH
552
A
HOH
49
4
HOH
HOH
553
A
HOH
50
4
HOH
HOH
554
A
HOH
51
4
HOH
HOH
555
A
HOH
52
4
HOH
HOH
556
A
HOH
53
4
HOH
HOH
557
A
HOH
54
4
HOH
HOH
558
A
HOH
55
4
HOH
HOH
559
A
HOH
56
4
HOH
HOH
560
A
HOH
57
4
HOH
HOH
561
A
HOH
58
4
HOH
HOH
562
A
HOH
59
4
HOH
HOH
563
A
HOH
60
4
HOH
HOH
564
A
HOH
61
4
HOH
HOH
565
A
HOH
62
4
HOH
HOH
566
A
HOH
63
4
HOH
HOH
567
A
HOH
64
4
HOH
HOH
568
A
HOH
65
4
HOH
HOH
569
A
HOH
66
4
HOH
HOH
570
A
HOH
67
4
HOH
HOH
571
A
HOH
68
4
HOH
HOH
572
A
HOH
69
4
HOH
HOH
573
A
HOH
70
4
HOH
HOH
574
A
HOH
71
4
HOH
HOH
575
A
HOH
72
4
HOH
HOH
576
A
HOH
73
4
HOH
HOH
577
A
HOH
74
4
HOH
HOH
578
A
HOH
75
4
HOH
HOH
579
A
HOH
76
4
HOH
HOH
580
A
HOH
77
4
HOH
HOH
581
A
HOH
78
4
HOH
HOH
582
A
HOH
79
4
HOH
HOH
583
A
HOH
80
4
HOH
HOH
584
A
HOH
81
4
HOH
HOH
585
A
HOH
82
4
HOH
HOH
586
A
HOH
83
4
HOH
HOH
587
A
HOH
84
4
HOH
HOH
588
A
HOH
85
4
HOH
HOH
589
A
HOH
86
4
HOH
HOH
590
A
HOH
87
4
HOH
HOH
591
A
HOH
88
4
HOH
HOH
592
A
HOH
89
4
HOH
HOH
593
A
HOH
90
4
HOH
HOH
594
A
HOH
91
4
HOH
HOH
595
A
HOH
92
4
HOH
HOH
596
A
HOH
93
4
HOH
HOH
597
A
HOH
94
4
HOH
HOH
598
A
HOH
95
4
HOH
HOH
599
A
HOH
96
4
HOH
HOH
600
A
HOH
97
4
HOH
HOH
601
A
HOH
98
4
HOH
HOH
602
A
HOH
99
4
HOH
HOH
603
A
HOH
100
4
HOH
HOH
604
A
n
1
0
A
LEU
1
n
2
LEU
1
A
ILE
2
n
3
ILE
2
A
VAL
3
n
4
VAL
3
A
LYS
4
n
5
LYS
4
A
ARG
5
n
6
ARG
5
A
GLY
6
n
7
GLY
6
A
ASP
7
n
8
ASP
7
A
VAL
8
n
9
VAL
8
A
TYR
9
n
10
TYR
9
A
PHE
10
n
11
PHE
10
A
ALA
11
n
12
ALA
11
A
ASP
12
n
13
ASP
12
A
LEU
13
n
14
LEU
13
A
SER
14
n
15
SER
14
A
PRO
15
n
16
PRO
15
A
VAL
16
n
17
VAL
16
A
VAL
17
n
18
VAL
17
A
GLY
18
n
19
GLY
18
A
SER
19
n
20
SER
19
A
GLU
20
n
21
GLU
20
A
GLN
21
n
22
GLN
21
A
GLY
22
n
23
GLY
22
A
GLY
23
n
24
GLY
23
A
VAL
24
n
25
VAL
24
A
ARG
25
n
26
ARG
25
A
PRO
26
n
27
PRO
26
A
VAL
27
n
28
VAL
27
A
LEU
28
n
29
LEU
28
A
VAL
29
n
30
VAL
29
A
ILE
30
n
31
ILE
30
A
GLN
31
n
32
GLN
31
A
ASN
32
n
33
ASN
32
A
ASP
33
n
34
ASP
33
A
ILE
34
n
35
ILE
34
A
GLY
35
n
36
GLY
35
A
ASN
36
n
37
ASN
36
A
ARG
37
n
38
ARG
37
A
PHE
38
n
39
PHE
38
A
SER
39
n
40
SER
39
A
PRO
40
n
41
PRO
40
A
THR
41
n
42
THR
41
A
ALA
42
n
43
ALA
42
A
ILE
43
n
44
ILE
43
A
VAL
44
n
45
VAL
44
A
ALA
45
n
46
ALA
45
A
ALA
46
n
47
ALA
46
A
ILE
47
n
48
ILE
47
A
THR
48
n
49
THR
48
A
ALA
49
n
50
ALA
49
A
GLN
50
n
51
GLN
50
A
ILE
51
n
52
ILE
51
A
GLN
52
n
53
GLN
52
A
LYS
53
n
54
LYS
53
A
ALA
54
n
55
ALA
54
A
LYS
55
n
56
LYS
55
A
LEU
56
n
57
LEU
56
A
PRO
57
n
58
PRO
57
A
THR
58
n
59
THR
58
A
HIS
59
n
60
HIS
59
A
VAL
60
n
61
VAL
60
A
GLU
61
n
62
GLU
61
A
ILE
62
n
63
ILE
62
A
ASP
63
n
64
ASP
63
A
ALA
64
n
65
ALA
64
A
LYS
65
n
66
LYS
65
A
ARG
66
n
67
ARG
66
A
TYR
67
n
68
TYR
67
A
GLY
68
n
69
GLY
68
A
PHE
69
n
70
PHE
69
A
GLU
70
n
71
GLU
70
A
ARG
71
n
72
ARG
71
A
ASP
72
n
73
ASP
72
A
SER
73
n
74
SER
73
A
VAL
74
n
75
VAL
74
A
ILE
75
n
76
ILE
75
A
LEU
76
n
77
LEU
76
A
LEU
77
n
78
LEU
77
A
GLU
78
n
79
GLU
78
A
GLN
79
n
80
GLN
79
A
ILE
80
n
81
ILE
80
A
ARG
81
n
82
ARG
81
A
THR
82
n
83
THR
82
A
ILE
83
n
84
ILE
83
A
ASP
84
n
85
ASP
84
A
LYS
85
n
86
LYS
85
A
GLN
86
n
87
GLN
86
A
ARG
87
n
88
ARG
87
A
LEU
88
n
89
LEU
88
A
THR
89
n
90
THR
89
A
ASP
90
n
91
ASP
90
A
LYS
91
n
92
LYS
91
A
ILE
92
n
93
ILE
92
A
THR
93
n
94
THR
93
A
HIS
94
n
95
HIS
94
A
LEU
95
n
96
LEU
95
A
ASP
96
n
97
ASP
96
A
ASP
97
n
98
ASP
97
A
GLU
98
n
99
GLU
98
A
MET
99
n
100
MET
99
A
MET
100
n
101
MET
100
A
ASP
101
n
102
ASP
101
A
LYS
102
n
103
LYS
102
A
VAL
103
n
104
VAL
103
A
ASP
104
n
105
ASP
104
A
GLU
105
n
106
GLU
105
A
ALA
106
n
107
ALA
106
A
LEU
107
n
108
LEU
107
A
GLN
108
n
109
GLN
108
A
ILE
109
n
110
ILE
109
A
SER
110
n
111
SER
110
A
LEU
111
n
112
LEU
111
A
ALA
112
n
113
ALA
112
A
LEU
113
n
114
LEU
113
A
ILE
114
n
115
ILE
114
A
ASP
115
n
116
ASP
115
A
PHE
116
n
117
PHE
116
A
author_defined_assembly
2
dimeric
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
10_665
-y+1,-x+1,-z+1/6
crystal symmetry operation
28.3150000000
49.0430186163
23.0428333333
A
N
ILE
62
A
N
ILE
63
A
O
SER
73
A
O
SER
74
A
O
ARG
81
A
O
ARG
82
A
N
VAL
44
A
N
VAL
45
A
O
ALA
45
A
O
ALA
46
A
N
LEU
28
A
N
LEU
29
A
O
VAL
27
A
O
VAL
28
A
N
TYR
9
A
N
TYR
10
A
N
VAL
8
A
N
VAL
9
A
O
ILE
92
A
O
ILE
93
1
A
HOH
582
F
HOH
1
A
HOH
592
F
HOH
1
A
CD
LYS
53
A
CD
LYS
54
1
Y
1
A
CE
LYS
53
A
CE
LYS
54
1
Y
1
A
NZ
LYS
53
A
NZ
LYS
54
1
Y
1
A
CG
LYS
65
A
CG
LYS
66
1
Y
1
A
CD
LYS
65
A
CD
LYS
66
1
Y
1
A
CE
LYS
65
A
CE
LYS
66
1
Y
1
A
NZ
LYS
65
A
NZ
LYS
66
1
Y
1
A
CZ
ARG
66
A
CZ
ARG
67
1
Y
1
A
NH1
ARG
66
A
NH1
ARG
67
1
Y
1
A
NH2
ARG
66
A
NH2
ARG
67
1
Y
1
A
C1
1PG
503
C
C1
1PG
1
1
N
1
A
C8
1PG
503
C
C8
1PG
1
1
N
1
A
C9
1PG
503
C
C9
1PG
1
1
N
1
A
O5
1PG
503
C
O5
1PG
1
1
N
1
A
C10
1PG
503
C
C10
1PG
1
1
N
1
A
C11
1PG
503
C
C11
1PG
1
1
N
1
A
O6
1PG
503
C
O6
1PG
1
1
N
1
A
SER
0
A
SER
1
1
Y
1
A
THR
89
-121.60
-97.87
22.098
0.02
0.01
0.0
0.02
0.0
-0.03
0.2097
0.1585
0.1619
0.1619
2.1
20.86
380
8204
8194
99.48
random
1
THROUGHOUT
0
MAD
Engh & Huber
2.1
20.86
108
1036
27
0
901
0.019
1.6
0.12
0.209
0.13
2.155
22
547
2.1
30
1NE8
8231
0.0
-3.0
0.058
0.058
1
19.6
9.8
99.5
0.17
2.1
2.18
8.86
794
0.17
98.5
data collection
MAR345
data scaling
SCALEPACK
phasing
SOLVE
model building
RESOLVE
refinement
REFMAC
phasing
RESOLVE
YDCE protein from Bacillus subtilis
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
4
N
N
The second molecule of the putative biological dimer is generated by the following transformation:
BIOMT1 0.5 -0.866 0.0 28.3175
BIOMT2 -0.866 -0.5 0.0 49.045
BIOMT3 0.0 0.0 -1.0 23.0431
A
ASN
32
A
ASN
33
HELX_P
A
SER
39
A
SER
40
1
1
8
A
ASP
63
A
ASP
64
HELX_P
A
GLY
68
A
GLY
69
1
2
6
A
ASP
96
A
ASP
97
HELX_P
A
LEU
111
A
LEU
112
1
3
16
STRUCTURAL GENOMICS, UNKNOWN FUNCTION
conserved hypothetical protein YDCE, STRUCTURAL GENOMICS, New York SGX Research Center for Structural Genomics, PSI, Protein Structure Initiative, NYSGXRC, UNKNOWN FUNCTION
A
SER
14
A
SER
15
1
A
PRO
15
A
PRO
16
-7.98
ENDOA_BACSU
UNP
1
2
P96622
IVKRGDVYFADLSPVVGSEQGGVRPVLVIQNDIGNRFSPTAIVAAITAQIQKAKLPTHVEIDAKRYGFERDSVILLEQIR
TIDKQRLTDKITHLDDEMMDKVDEALQISLALIDF
2
116
1NE8
2
116
P96622
A
1
3
117
1
cloning artifact
SER
0
1NE8
A
P96622
UNP
1
1
cloning artifact
LEU
1
1NE8
A
P96622
UNP
2
6
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
HIS
59
A
HIS
60
A
ILE
62
A
ILE
63
A
SER
73
A
SER
74
A
ASP
84
A
ASP
85
A
THR
41
A
THR
42
A
THR
48
A
THR
49
A
VAL
24
A
VAL
25
A
VAL
29
A
VAL
30
A
ASP
7
A
ASP
8
A
ASP
12
A
ASP
13
A
LEU
88
A
LEU
89
A
HIS
94
A
HIS
95
BINDING SITE FOR RESIDUE 1PG A 501
A
1PG
501
Software
10
BINDING SITE FOR RESIDUE 1PG A 503
A
1PG
503
Software
4
BINDING SITE FOR RESIDUE ACY A 502
A
ACY
502
Software
6
BINDING SITE FOR RESIDUE ACY A 504
A
ACY
504
Software
3
A
ALA
49
A
ALA
50
10
6_654
A
GLN
50
A
GLN
51
10
9_655
A
ARG
71
A
ARG
72
10
6_654
A
GLU
105
A
GLU
106
10
1_555
A
GLN
108
A
GLN
109
10
1_555
A
ILE
114
A
ILE
115
10
10_665
A
ASP
115
A
ASP
116
10
10_665
A
ASP
115
A
ASP
116
10
1_555
A
PHE
116
A
PHE
117
10
1_555
A
HOH
559
F
HOH
10
1_555
A
SER
14
A
SER
15
4
1_555
A
VAL
17
A
VAL
18
4
10_665
A
HOH
585
F
HOH
4
9_665
A
HOH
601
F
HOH
4
1_555
A
PRO
26
A
PRO
27
6
1_555
A
PHE
69
A
PHE
70
6
1_555
A
GLU
70
A
GLU
71
6
1_555
A
ILE
114
A
ILE
115
6
9_665
A
HOH
564
F
HOH
6
1_555
A
HOH
580
F
HOH
6
1_555
A
PHE
38
A
PHE
39
3
5_565
A
LYS
91
A
LYS
92
3
1_555
A
ILE
92
A
ILE
93
3
1_555
179
P 65 2 2