0.024773
0.000000
0.000000
0.000000
0.015428
0.000000
0.000000
0.000000
0.013654
0.00000
0.00000
0.00000
Fedorov, A.A.
Fedorov, E.V.
Desai, B.
Gerlt, J.A.
Almo, S.C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
40.367
64.819
73.237
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
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
O4 S -2
96.063
SULFATE ION
non-polymer
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
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
N
N
251
S
C
N
252
N
C
N
253
N
O
N
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
N
261
N
O
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
H
N
273
N
N
N
274
S
C
N
275
N
C
N
276
N
O
N
277
N
C
N
278
N
C
N
279
N
C
N
280
N
O
N
281
N
H
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
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
N
C
N
295
N
O
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
S
N
305
N
O
N
306
N
O
N
307
N
O
N
308
N
O
N
309
N
N
N
310
S
C
N
311
N
C
N
312
N
O
N
313
R
C
N
314
N
O
N
315
N
C
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
H
N
325
N
H
N
326
N
N
N
327
S
C
N
328
N
C
N
329
N
O
N
330
N
C
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
N
Y
335
N
C
Y
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
C
N
340
N
O
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
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
N
N
354
S
C
N
355
N
C
N
356
N
O
N
357
N
C
Y
358
N
C
Y
359
N
C
Y
360
N
C
Y
361
N
C
Y
362
N
C
Y
363
N
C
N
364
N
O
N
365
N
O
N
366
N
H
N
367
N
H
N
368
N
H
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
N
N
378
S
C
N
379
N
C
N
380
N
O
N
381
N
C
N
382
N
C
N
383
N
C
N
384
N
O
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
H
N
395
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
doub
N
291
N
doub
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
doub
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
Y
321
N
doub
Y
322
N
sing
Y
323
N
sing
N
324
N
sing
Y
325
N
doub
Y
326
N
sing
Y
327
N
sing
N
328
N
sing
Y
329
N
sing
Y
330
N
doub
N
331
N
sing
Y
332
N
doub
N
333
N
sing
Y
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
doub
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
Y
349
N
doub
Y
350
N
sing
Y
351
N
sing
N
352
N
sing
Y
353
N
doub
N
354
N
sing
Y
355
N
doub
N
356
N
sing
Y
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
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
doub
N
369
N
sing
N
370
N
sing
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
To be Published
0353
Crystal structure of orotidine 5'-monophosphate decarboxylase from Sulfolobus solfataricus
10.2210/pdb4dbd/pdb
pdb_00004dbd
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
2010-11-05
ADSC QUANTUM 315r
MIRRORS
SINGLE WAVELENGTH
M
x-ray
1
1.075
1.0
X29A
NSLS
1.075
SYNCHROTRON
NSLS BEAMLINE X29A
24733.945
Orotidine 5'-phosphate decarboxylase
4.1.1.23
1
man
polymer
96.063
SULFATE ION
3
syn
non-polymer
18.015
water
82
nat
water
OMP decarboxylase
no
no
MLKSRVILAMDKPLSYQVLKEMENELYGIKVGLPLVLDLGVDKTRELLIGLDVEEIIVDFKLADIGYIMKSIVERLSFAN
SFIAHSFIGVKGSLDELKRYLDANSKNLYLVAVMSHEGWSTLFADYIKNVIREISPKGIVVGGTKLDHITQYRRDFEKMT
IVSPGMGSQGGSYGDAVCAGADYEIIGRSIYNAGNPLTALRTINKIIEDKVMKCKGAIFRKK
MLKSRVILAMDKPLSYQVLKEMENELYGIKVGLPLVLDLGVDKTRELLIGLDVEEIIVDFKLADIGYIMKSIVERLSFAN
SFIAHSFIGVKGSLDELKRYLDANSKNLYLVAVMSHEGWSTLFADYIKNVIREISPKGIVVGGTKLDHITQYRRDFEKMT
IVSPGMGSQGGSYGDAVCAGADYEIIGRSIYNAGNPLTALRTINKIIEDKVMKCKGAIFRKK
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
98/2
sample
pyrF, Ssol_1680
555311
Sulfolobus solfataricus
562
Escherichia coli
1
1.94
36.50
VAPOR DIFFUSION, HANGING DROP
5.6
1.0M lithium sulfate, 0.1M sodium citrate, 0.5M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
293.0
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_site
repository
Initial release
Data collection
Database references
Derived calculations
Refinement description
1
0
2013-02-13
1
1
2023-09-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2012-01-14
REL
REL
SO4
SULFATE ION
HOH
water
3VE9
PDB
experimental model
SO4
1
2
SO4
SO4
301
A
SO4
2
2
SO4
SO4
302
A
SO4
1
2
SO4
SO4
303
A
HOH
1
3
HOH
HOH
401
A
HOH
2
3
HOH
HOH
402
A
HOH
3
3
HOH
HOH
403
A
HOH
4
3
HOH
HOH
404
A
HOH
5
3
HOH
HOH
405
A
HOH
6
3
HOH
HOH
406
A
HOH
7
3
HOH
HOH
407
A
HOH
8
3
HOH
HOH
408
A
HOH
9
3
HOH
HOH
409
A
HOH
10
3
HOH
HOH
410
A
HOH
11
3
HOH
HOH
411
A
HOH
12
3
HOH
HOH
412
A
HOH
13
3
HOH
HOH
413
A
HOH
14
3
HOH
HOH
414
A
HOH
15
3
HOH
HOH
415
A
HOH
16
3
HOH
HOH
416
A
HOH
17
3
HOH
HOH
417
A
HOH
18
3
HOH
HOH
418
A
HOH
19
3
HOH
HOH
419
A
HOH
20
3
HOH
HOH
420
A
HOH
21
3
HOH
HOH
421
A
HOH
22
3
HOH
HOH
422
A
HOH
23
3
HOH
HOH
423
A
HOH
24
3
HOH
HOH
424
A
HOH
25
3
HOH
HOH
425
A
HOH
26
3
HOH
HOH
426
A
HOH
27
3
HOH
HOH
427
A
HOH
28
3
HOH
HOH
428
A
HOH
29
3
HOH
HOH
429
A
HOH
30
3
HOH
HOH
430
A
HOH
31
3
HOH
HOH
431
A
HOH
32
3
HOH
HOH
432
A
HOH
33
3
HOH
HOH
433
A
HOH
34
3
HOH
HOH
434
A
HOH
35
3
HOH
HOH
435
A
HOH
36
3
HOH
HOH
436
A
HOH
37
3
HOH
HOH
437
A
HOH
38
3
HOH
HOH
438
A
HOH
39
3
HOH
HOH
439
A
HOH
40
3
HOH
HOH
440
A
HOH
41
3
HOH
HOH
441
A
HOH
42
3
HOH
HOH
442
A
HOH
43
3
HOH
HOH
443
A
HOH
44
3
HOH
HOH
444
A
HOH
45
3
HOH
HOH
445
A
HOH
47
3
HOH
HOH
446
A
HOH
48
3
HOH
HOH
447
A
HOH
49
3
HOH
HOH
448
A
HOH
50
3
HOH
HOH
449
A
HOH
51
3
HOH
HOH
450
A
HOH
52
3
HOH
HOH
451
A
HOH
53
3
HOH
HOH
452
A
HOH
54
3
HOH
HOH
453
A
HOH
55
3
HOH
HOH
454
A
HOH
56
3
HOH
HOH
455
A
HOH
57
3
HOH
HOH
456
A
HOH
58
3
HOH
HOH
457
A
HOH
59
3
HOH
HOH
458
A
HOH
60
3
HOH
HOH
459
A
HOH
61
3
HOH
HOH
460
A
HOH
63
3
HOH
HOH
461
A
HOH
64
3
HOH
HOH
462
A
HOH
65
3
HOH
HOH
463
A
HOH
66
3
HOH
HOH
464
A
HOH
67
3
HOH
HOH
465
A
HOH
68
3
HOH
HOH
466
A
HOH
69
3
HOH
HOH
467
A
HOH
70
3
HOH
HOH
468
A
HOH
71
3
HOH
HOH
469
A
HOH
72
3
HOH
HOH
470
A
HOH
73
3
HOH
HOH
471
A
HOH
74
3
HOH
HOH
472
A
HOH
75
3
HOH
HOH
473
A
HOH
76
3
HOH
HOH
474
A
HOH
77
3
HOH
HOH
475
A
HOH
78
3
HOH
HOH
476
A
HOH
79
3
HOH
HOH
477
A
HOH
80
3
HOH
HOH
478
A
HOH
81
3
HOH
HOH
479
A
HOH
82
3
HOH
HOH
480
A
HOH
83
3
HOH
HOH
481
A
HOH
84
3
HOH
HOH
482
A
n
1
1
A
n
2
2
A
LYS
3
n
3
LYS
3
A
SER
4
n
4
SER
4
A
ARG
5
n
5
ARG
5
A
VAL
6
n
6
VAL
6
A
ILE
7
n
7
ILE
7
A
LEU
8
n
8
LEU
8
A
ALA
9
n
9
ALA
9
A
MET
10
n
10
MET
10
A
ASP
11
n
11
ASP
11
A
LYS
12
n
12
LYS
12
A
PRO
13
n
13
PRO
13
A
LEU
14
n
14
LEU
14
A
SER
15
n
15
SER
15
A
TYR
16
n
16
TYR
16
A
GLN
17
n
17
GLN
17
A
VAL
18
n
18
VAL
18
A
LEU
19
n
19
LEU
19
A
LYS
20
n
20
LYS
20
A
GLU
21
n
21
GLU
21
A
MET
22
n
22
MET
22
A
GLU
23
n
23
GLU
23
A
ASN
24
n
24
ASN
24
A
GLU
25
n
25
GLU
25
A
LEU
26
n
26
LEU
26
A
TYR
27
n
27
TYR
27
A
GLY
28
n
28
GLY
28
A
ILE
29
n
29
ILE
29
A
LYS
30
n
30
LYS
30
A
VAL
31
n
31
VAL
31
A
GLY
32
n
32
GLY
32
A
LEU
33
n
33
LEU
33
A
PRO
34
n
34
PRO
34
A
LEU
35
n
35
LEU
35
A
VAL
36
n
36
VAL
36
A
LEU
37
n
37
LEU
37
A
ASP
38
n
38
ASP
38
A
LEU
39
n
39
LEU
39
A
GLY
40
n
40
GLY
40
A
VAL
41
n
41
VAL
41
A
ASP
42
n
42
ASP
42
A
LYS
43
n
43
LYS
43
A
THR
44
n
44
THR
44
A
ARG
45
n
45
ARG
45
A
GLU
46
n
46
GLU
46
A
LEU
47
n
47
LEU
47
A
LEU
48
n
48
LEU
48
A
ILE
49
n
49
ILE
49
A
GLY
50
n
50
GLY
50
A
LEU
51
n
51
LEU
51
A
ASP
52
n
52
ASP
52
A
VAL
53
n
53
VAL
53
A
GLU
54
n
54
GLU
54
A
GLU
55
n
55
GLU
55
A
ILE
56
n
56
ILE
56
A
ILE
57
n
57
ILE
57
A
VAL
58
n
58
VAL
58
A
ASP
59
n
59
ASP
59
A
PHE
60
n
60
PHE
60
A
LYS
61
n
61
LYS
61
A
LEU
62
n
62
LEU
62
A
ALA
63
n
63
ALA
63
A
ASP
64
n
64
ASP
64
A
ILE
65
n
65
ILE
65
A
GLY
66
n
66
GLY
66
A
TYR
67
n
67
TYR
67
A
ILE
68
n
68
ILE
68
A
MET
69
n
69
MET
69
A
LYS
70
n
70
LYS
70
A
SER
71
n
71
SER
71
A
ILE
72
n
72
ILE
72
A
VAL
73
n
73
VAL
73
A
GLU
74
n
74
GLU
74
A
ARG
75
n
75
ARG
75
A
LEU
76
n
76
LEU
76
A
SER
77
n
77
SER
77
A
PHE
78
n
78
PHE
78
A
ALA
79
n
79
ALA
79
A
ASN
80
n
80
ASN
80
A
SER
81
n
81
SER
81
A
PHE
82
n
82
PHE
82
A
ILE
83
n
83
ILE
83
A
ALA
84
n
84
ALA
84
A
HIS
85
n
85
HIS
85
A
SER
86
n
86
SER
86
A
PHE
87
n
87
PHE
87
A
ILE
88
n
88
ILE
88
A
GLY
89
n
89
GLY
89
A
VAL
90
n
90
VAL
90
A
LYS
91
n
91
LYS
91
A
GLY
92
n
92
GLY
92
A
SER
93
n
93
SER
93
A
LEU
94
n
94
LEU
94
A
ASP
95
n
95
ASP
95
A
GLU
96
n
96
GLU
96
A
LEU
97
n
97
LEU
97
A
LYS
98
n
98
LYS
98
A
ARG
99
n
99
ARG
99
A
TYR
100
n
100
TYR
100
A
LEU
101
n
101
LEU
101
A
ASP
102
n
102
ASP
102
A
ALA
103
n
103
ALA
103
A
ASN
104
n
104
ASN
104
A
SER
105
n
105
SER
105
A
LYS
106
n
106
LYS
106
A
ASN
107
n
107
ASN
107
A
LEU
108
n
108
LEU
108
A
TYR
109
n
109
TYR
109
A
LEU
110
n
110
LEU
110
A
VAL
111
n
111
VAL
111
A
ALA
112
n
112
ALA
112
A
VAL
113
n
113
VAL
113
A
MET
114
n
114
MET
114
A
SER
115
n
115
SER
115
A
HIS
116
n
116
HIS
116
A
GLU
117
n
117
GLU
117
A
GLY
118
n
118
GLY
118
A
TRP
119
n
119
TRP
119
A
SER
120
n
120
SER
120
A
THR
121
n
121
THR
121
A
LEU
122
n
122
LEU
122
A
PHE
123
n
123
PHE
123
A
ALA
124
n
124
ALA
124
A
ASP
125
n
125
ASP
125
A
TYR
126
n
126
TYR
126
A
ILE
127
n
127
ILE
127
A
LYS
128
n
128
LYS
128
A
ASN
129
n
129
ASN
129
A
VAL
130
n
130
VAL
130
A
ILE
131
n
131
ILE
131
A
ARG
132
n
132
ARG
132
A
GLU
133
n
133
GLU
133
A
ILE
134
n
134
ILE
134
A
SER
135
n
135
SER
135
A
PRO
136
n
136
PRO
136
A
LYS
137
n
137
LYS
137
A
GLY
138
n
138
GLY
138
A
ILE
139
n
139
ILE
139
A
VAL
140
n
140
VAL
140
A
VAL
141
n
141
VAL
141
A
GLY
142
n
142
GLY
142
A
GLY
143
n
143
GLY
143
A
THR
144
n
144
THR
144
A
LYS
145
n
145
LYS
145
A
LEU
146
n
146
LEU
146
A
ASP
147
n
147
ASP
147
A
HIS
148
n
148
HIS
148
A
ILE
149
n
149
ILE
149
A
THR
150
n
150
THR
150
A
GLN
151
n
151
GLN
151
A
TYR
152
n
152
TYR
152
A
ARG
153
n
153
ARG
153
A
ARG
154
n
154
ARG
154
A
ASP
155
n
155
ASP
155
A
PHE
156
n
156
PHE
156
A
GLU
157
n
157
GLU
157
A
LYS
158
n
158
LYS
158
A
MET
159
n
159
MET
159
A
THR
160
n
160
THR
160
A
ILE
161
n
161
ILE
161
A
VAL
162
n
162
VAL
162
A
SER
163
n
163
SER
163
A
PRO
164
n
164
PRO
164
A
GLY
165
n
165
GLY
165
A
MET
166
n
166
MET
166
A
GLY
167
n
167
GLY
167
A
SER
168
n
168
SER
168
A
GLN
169
n
169
GLN
169
A
GLY
170
n
170
GLY
170
A
GLY
171
n
171
GLY
171
A
SER
172
n
172
SER
172
A
TYR
173
n
173
TYR
173
A
GLY
174
n
174
GLY
174
A
ASP
175
n
175
ASP
175
A
ALA
176
n
176
ALA
176
A
VAL
177
n
177
VAL
177
A
CYS
178
n
178
CYS
178
A
ALA
179
n
179
ALA
179
A
GLY
180
n
180
GLY
180
A
ALA
181
n
181
ALA
181
A
ASP
182
n
182
ASP
182
A
TYR
183
n
183
TYR
183
A
GLU
184
n
184
GLU
184
A
ILE
185
n
185
ILE
185
A
ILE
186
n
186
ILE
186
A
GLY
187
n
187
GLY
187
A
ARG
188
n
188
ARG
188
A
SER
189
n
189
SER
189
A
ILE
190
n
190
ILE
190
A
TYR
191
n
191
TYR
191
A
ASN
192
n
192
ASN
192
A
ALA
193
n
193
ALA
193
A
GLY
194
n
194
GLY
194
A
ASN
195
n
195
ASN
195
A
PRO
196
n
196
PRO
196
A
LEU
197
n
197
LEU
197
A
THR
198
n
198
THR
198
A
ALA
199
n
199
ALA
199
A
LEU
200
n
200
LEU
200
A
ARG
201
n
201
ARG
201
A
THR
202
n
202
THR
202
A
ILE
203
n
203
ILE
203
A
ASN
204
n
204
ASN
204
A
LYS
205
n
205
LYS
205
A
ILE
206
n
206
ILE
206
A
ILE
207
n
207
ILE
207
A
GLU
208
n
208
GLU
208
A
ASP
209
n
209
ASP
209
A
LYS
210
n
210
LYS
210
A
VAL
211
n
211
VAL
211
A
MET
212
n
212
MET
212
A
n
213
213
A
n
214
214
A
n
215
215
A
n
216
216
A
n
217
217
A
n
218
218
A
n
219
219
A
n
220
220
A
n
221
221
A
n
222
222
A
author_and_software_defined_assembly
PISA
2
dimeric
4780
-129
15860
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_555
-x,-y,z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
A
N
LEU
8
A
N
LEU
8
A
O
LYS
30
A
O
LYS
30
A
N
VAL
31
A
N
VAL
31
A
O
ILE
57
A
O
ILE
57
A
N
LEU
62
A
N
LEU
62
A
O
HIS
85
A
O
HIS
85
A
N
PHE
82
A
N
PHE
82
A
O
TYR
109
A
O
TYR
109
A
N
ALA
112
A
N
ALA
112
A
O
VAL
140
A
O
VAL
140
A
N
VAL
141
A
N
VAL
141
A
O
VAL
162
A
O
VAL
162
A
N
SER
163
A
N
SER
163
A
O
ILE
185
A
O
ILE
185
A
O
GLU
184
A
O
GLU
184
A
N
ILE
7
A
N
ILE
7
1
A
SO4
303
D
SO4
1
A
MET
1
A
MET
1
1
Y
1
A
LEU
2
A
LEU
2
1
Y
1
A
LYS
213
A
LYS
213
1
Y
1
A
CYS
214
A
CYS
214
1
Y
1
A
LYS
215
A
LYS
215
1
Y
1
A
GLY
216
A
GLY
216
1
Y
1
A
ALA
217
A
ALA
217
1
Y
1
A
ILE
218
A
ILE
218
1
Y
1
A
PHE
219
A
PHE
219
1
Y
1
A
ARG
220
A
ARG
220
1
Y
1
A
LYS
221
A
LYS
221
1
Y
1
A
LYS
222
A
LYS
222
1
Y
1
A
ALA
63
-156.98
62.42
1
A
VAL
90
-97.73
-66.40
1
A
SER
93
-138.56
-91.54
1
A
LYS
145
-108.24
65.85
-4.7229
0.0000
-0.0000
10.7679
-0.0000
-6.0450
0.2450
0.2078
0.2097
0.2097
1.699
36.618
1107
21586
21586
5.13
98.82
0.43
RANDOM
1
0.0
MOLECULAR REPLACEMENT
25.41
1.17
1.40
3VE9
ML
FLAT BULK SOLVENT MODEL
29.097
0.360
1.699
36.618
82
1733
15
0
1636
0.006
1705
0.992
2303
13.397
638
0.071
262
0.004
289
0.3604
0.3067
1.7767
122
2320
91.00
0.3045
0.2612
1.8703
128
2528
100.00
0.2773
0.2147
1.9875
157
2539
100.00
0.2459
0.2141
2.1410
132
2573
100.00
0.2784
0.2114
2.3564
141
2561
100.00
0.3078
0.2129
2.6973
154
2587
100.00
0.2116
0.2122
3.3979
135
2614
100.00
0.2007
0.1832
36.6270
138
2757
100.00
1.699
36.618
4DBD
21586
21586
0.0
0.0
1
98.82
data collection
CBASS
model building
PHENIX
refinement
PHENIX
(phenix.refine: 1.7.1_743)
data reduction
HKL-2000
data scaling
HKL-2000
phasing
PHENIX
Crystal structure of orotidine 5'-monophosphate decarboxylase from Sulfolobus solfataricus
1
N
N
2
N
N
2
N
N
2
N
N
3
N
N
A
SER
15
A
SER
15
HELX_P
A
GLU
23
A
GLU
23
1
1
9
A
ASN
24
A
ASN
24
HELX_P
A
LEU
26
A
LEU
26
5
2
3
A
LEU
33
A
LEU
33
HELX_P
A
GLY
40
A
GLY
40
1
3
8
A
GLY
40
A
GLY
40
HELX_P
A
ILE
49
A
ILE
49
1
4
10
A
ILE
65
A
ILE
65
HELX_P
A
GLU
74
A
GLU
74
1
5
10
A
SER
93
A
SER
93
HELX_P
A
ASN
104
A
ASN
104
1
6
12
A
PHE
123
A
PHE
123
HELX_P
A
SER
135
A
SER
135
1
7
13
A
LYS
145
A
LYS
145
HELX_P
A
PHE
156
A
PHE
156
1
8
12
A
GLY
174
A
GLY
174
HELX_P
A
GLY
180
A
GLY
180
1
9
7
A
GLY
187
A
GLY
187
HELX_P
A
ASN
192
A
ASN
192
1
10
6
A
ASN
195
A
ASN
195
HELX_P
A
VAL
211
A
VAL
211
1
11
17
LYASE
TIM barrel, orotidine 5'-monophosphate decarboxylase, orotidine 5'-monophosphate, LYASE
D0KT28_SULS9
UNP
1
1
D0KT28
MLKSRVILAMDKPLSYQVLKEMENELYGIKVGLPLVLDLGVDKTRELLIGLDVEEIIVDFKLADIGYIMKSIVERLSFAN
SFIAHSFIGVKGSLDELKRYLDANSKNLYLVAVMSHEGWSTLFADYIKNVIREISPKGIVVGGTKLDHITQYRRDFEKMT
IVSPGMGSQGGSYGDAVCAGADYEIIGRSIYNAGNPLTALRTINKIIEDKVMKCKGAIFRKK
1
222
4DBD
1
222
D0KT28
A
1
1
222
9
parallel
parallel
parallel
parallel
parallel
parallel
parallel
parallel
A
VAL
6
A
VAL
6
A
MET
10
A
MET
10
A
GLY
28
A
GLY
28
A
GLY
32
A
GLY
32
A
GLU
55
A
GLU
55
A
LEU
62
A
LEU
62
A
SER
81
A
SER
81
A
HIS
85
A
HIS
85
A
ASN
107
A
ASN
107
A
VAL
113
A
VAL
113
A
GLY
138
A
GLY
138
A
VAL
141
A
VAL
141
A
THR
160
A
THR
160
A
SER
163
A
SER
163
A
TYR
183
A
TYR
183
A
ILE
186
A
ILE
186
A
VAL
6
A
VAL
6
A
MET
10
A
MET
10
BINDING SITE FOR RESIDUE SO4 A 301
A
SO4
301
Software
7
BINDING SITE FOR RESIDUE SO4 A 302
A
SO4
302
Software
2
BINDING SITE FOR RESIDUE SO4 A 303
A
SO4
303
Software
6
A
GLN
169
A
GLN
169
7
1_555
A
GLY
187
A
GLY
187
7
1_555
A
ARG
188
A
ARG
188
7
1_555
A
HOH
407
E
HOH
7
1_555
A
HOH
419
E
HOH
7
1_555
A
HOH
431
E
HOH
7
1_555
A
HOH
451
E
HOH
7
1_555
A
THR
121
A
THR
121
2
1_555
A
HIS
148
A
HIS
148
2
1_555
A
GLY
40
A
GLY
40
6
2_555
A
GLY
40
A
GLY
40
6
1_555
A
VAL
41
A
VAL
41
6
1_555
A
VAL
41
A
VAL
41
6
2_555
A
HOH
438
E
HOH
6
2_555
A
HOH
438
E
HOH
6
1_555
18
P 21 21 2