0.018504
0.000000
0.000000
0.000000
0.010732
0.000000
0.000000
0.000000
0.009484
0.00000
0.00000
0.00000
2.3100
1.0200
1.5886
0.8650
20.8439
10.2075
0.5687
51.6512
0.2156
11.4604
7.1964
6.2556
1.6455
0.0104
1.1662
18.5194
47.7784
-9.3663
0.2599
0.1911
0.4930
0.3229
0.1402
0.0408
10.5109
26.1257
3.1424
57.7997
0.0030
12.2126
3.1322
2.0125
1.1663
0.0057
9.8933
28.9975
0.5826
-11.5290
3.0485
2.2868
1.5463
0.8670
13.2771
5.7011
0.3239
32.9089
0.2508
6.9053
5.2034
1.4379
1.5863
1.4679
22.2151
0.2536
56.1720
1.0297
0.2033
0.1628
17.0006
5.8196
3.9731
4.3543
2.4098
0.2726
15.2372
43.8163
1.0272
3.3514
-1.8137
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.000
90.000
90.000
54.041
93.178
105.443
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
Cl -1
35.453
CHLORIDE ION
non-polymer
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 Se
196.106
n
SELENOMETHIONINE
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
To be published
0353
Crystal structure of the apo form of a 3alpha-hydroxysteroid dehydrogenase (BaiA2) associated with secondary bile acid synthesis from Clostridium scindens VPI12708 at 1.90 A resolution
10.2210/pdb4is2/pdb
pdb_00004is2
100
1
double crystal monochromator
CCD
2010-05-13
MARMOSAIC 325 mm CCD
double crystal
MAD
M
x-ray
1
0.91162
1.0
0.97934
1.0
0.97915
1.0
BL9-2
SSRL
0.91162, 0.97934, 0.97915
SYNCHROTRON
SSRL BEAMLINE BL9-2
29344.883
Bile acid 3-alpha hydroxysteroid dehydrogenase
1
man
polymer
35.453
CHLORIDE ION
1
syn
non-polymer
18.015
water
101
nat
water
no
yes
(MSE)GSDKIHHHHHHENLYFQG(MSE)NLVQDKVTIITGGTRGIGFAAAKIFIDNGAKVSIFGETQEEVDTALAQLKEL
YPEEEVLGFAPDLTSRDAV(MSE)AAVGQVAQKYGRLDV(MSE)INNAGITSNNVFSRVSEEEFKHI(MSE)DINVTGVF
NGAWCAYQC(MSE)KDAKKGVIINTASVTGIFGSLSGVGYPASKASVIGLTHGLGREIIRKNIRVVGVAPGVVNTD
(MSE)TNGNPPEI(MSE)EGYLKALP(MSE)KR(MSE)LEPEEIANVYLFLASDLASGITATTVSVDGAYRP
MGSDKIHHHHHHENLYFQGMNLVQDKVTIITGGTRGIGFAAAKIFIDNGAKVSIFGETQEEVDTALAQLKELYPEEEVLG
FAPDLTSRDAVMAAVGQVAQKYGRLDVMINNAGITSNNVFSRVSEEEFKHIMDINVTGVFNGAWCAYQCMKDAKKGVIIN
TASVTGIFGSLSGVGYPASKASVIGLTHGLGREIIRKNIRVVGVAPGVVNTDMTNGNPPEIMEGYLKALPMKRMLEPEEI
ANVYLFLASDLASGITATTVSVDGAYRP
A
JCSG-420767
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
VPI 12708
sample
The source organism was previously designated Eubacterium sp. (strain VPI 12708).
baiA, BAIA2
29347
Clostridium scindens
562
Escherichia Coli
HK100
Plasmid
SpeedET
1
2.26
45.62
VAPOR DIFFUSION, SITTING DROP
4.5
0.1M sodium acetate pH 4.5, 2.5M sodium chloride, 0.2M lithium sulfate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
Joint Center for Structural Genomics
JCSG
PSI:Biology
software
citation_author
database_2
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Structure summary
Refinement description
Database references
Database references
Derived calculations
1
0
2013-04-03
1
1
2013-09-04
1
2
2017-11-15
1
3
2018-01-24
1
4
2023-02-01
_software.classification
_software.name
_citation_author.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Holoenzyme form of BaiA2 (a 3alpha-hydroxysteroid dehydrogenase ssociated with secondary bile acid synthesis from Clostridium scindens VPI12708) in complex with a putative NAD(+)OH- adduct at 2.0 A resolution
Y
RCSB
Y
RCSB
2013-01-16
REL
REL
CL
CHLORIDE ION
HOH
water
THIS CONSTRUCT (RESIDUES 1-249) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG.
CL
250
2
CL
CL
301
A
HOH
251
3
HOH
HOH
401
A
HOH
252
3
HOH
HOH
402
A
HOH
253
3
HOH
HOH
403
A
HOH
254
3
HOH
HOH
404
A
HOH
255
3
HOH
HOH
405
A
HOH
256
3
HOH
HOH
406
A
HOH
257
3
HOH
HOH
407
A
HOH
258
3
HOH
HOH
408
A
HOH
259
3
HOH
HOH
409
A
HOH
260
3
HOH
HOH
410
A
HOH
261
3
HOH
HOH
411
A
HOH
262
3
HOH
HOH
412
A
HOH
263
3
HOH
HOH
413
A
HOH
264
3
HOH
HOH
414
A
HOH
265
3
HOH
HOH
415
A
HOH
266
3
HOH
HOH
416
A
HOH
267
3
HOH
HOH
417
A
HOH
268
3
HOH
HOH
418
A
HOH
269
3
HOH
HOH
419
A
HOH
270
3
HOH
HOH
420
A
HOH
271
3
HOH
HOH
421
A
HOH
272
3
HOH
HOH
422
A
HOH
273
3
HOH
HOH
423
A
HOH
274
3
HOH
HOH
424
A
HOH
275
3
HOH
HOH
425
A
HOH
276
3
HOH
HOH
426
A
HOH
277
3
HOH
HOH
427
A
HOH
278
3
HOH
HOH
428
A
HOH
279
3
HOH
HOH
429
A
HOH
280
3
HOH
HOH
430
A
HOH
281
3
HOH
HOH
431
A
HOH
282
3
HOH
HOH
432
A
HOH
283
3
HOH
HOH
433
A
HOH
284
3
HOH
HOH
434
A
HOH
285
3
HOH
HOH
435
A
HOH
286
3
HOH
HOH
436
A
HOH
287
3
HOH
HOH
437
A
HOH
288
3
HOH
HOH
438
A
HOH
289
3
HOH
HOH
439
A
HOH
290
3
HOH
HOH
440
A
HOH
291
3
HOH
HOH
441
A
HOH
292
3
HOH
HOH
442
A
HOH
293
3
HOH
HOH
443
A
HOH
294
3
HOH
HOH
444
A
HOH
295
3
HOH
HOH
445
A
HOH
296
3
HOH
HOH
446
A
HOH
297
3
HOH
HOH
447
A
HOH
298
3
HOH
HOH
448
A
HOH
299
3
HOH
HOH
449
A
HOH
300
3
HOH
HOH
450
A
HOH
301
3
HOH
HOH
451
A
HOH
302
3
HOH
HOH
452
A
HOH
303
3
HOH
HOH
453
A
HOH
304
3
HOH
HOH
454
A
HOH
305
3
HOH
HOH
455
A
HOH
306
3
HOH
HOH
456
A
HOH
307
3
HOH
HOH
457
A
HOH
308
3
HOH
HOH
458
A
HOH
309
3
HOH
HOH
459
A
HOH
310
3
HOH
HOH
460
A
HOH
311
3
HOH
HOH
461
A
HOH
312
3
HOH
HOH
462
A
HOH
313
3
HOH
HOH
463
A
HOH
314
3
HOH
HOH
464
A
HOH
315
3
HOH
HOH
465
A
HOH
316
3
HOH
HOH
466
A
HOH
317
3
HOH
HOH
467
A
HOH
318
3
HOH
HOH
468
A
HOH
319
3
HOH
HOH
469
A
HOH
320
3
HOH
HOH
470
A
HOH
321
3
HOH
HOH
471
A
HOH
322
3
HOH
HOH
472
A
HOH
323
3
HOH
HOH
473
A
HOH
324
3
HOH
HOH
474
A
HOH
325
3
HOH
HOH
475
A
HOH
326
3
HOH
HOH
476
A
HOH
327
3
HOH
HOH
477
A
HOH
328
3
HOH
HOH
478
A
HOH
329
3
HOH
HOH
479
A
HOH
330
3
HOH
HOH
480
A
HOH
331
3
HOH
HOH
481
A
HOH
332
3
HOH
HOH
482
A
HOH
333
3
HOH
HOH
483
A
HOH
334
3
HOH
HOH
484
A
HOH
335
3
HOH
HOH
485
A
HOH
336
3
HOH
HOH
486
A
HOH
337
3
HOH
HOH
487
A
HOH
338
3
HOH
HOH
488
A
HOH
339
3
HOH
HOH
489
A
HOH
340
3
HOH
HOH
490
A
HOH
341
3
HOH
HOH
491
A
HOH
342
3
HOH
HOH
492
A
HOH
343
3
HOH
HOH
493
A
HOH
344
3
HOH
HOH
494
A
HOH
345
3
HOH
HOH
495
A
HOH
346
3
HOH
HOH
496
A
HOH
347
3
HOH
HOH
497
A
HOH
348
3
HOH
HOH
498
A
HOH
349
3
HOH
HOH
499
A
HOH
350
3
HOH
HOH
500
A
HOH
351
3
HOH
HOH
501
A
n
1
-18
A
n
2
-17
A
n
3
-16
A
n
4
-15
A
n
5
-14
A
n
6
-13
A
n
7
-12
A
n
8
-11
A
n
9
-10
A
n
10
-9
A
n
11
-8
A
n
12
-7
A
n
13
-6
A
n
14
-5
A
n
15
-4
A
n
16
-3
A
n
17
-2
A
n
18
-1
A
n
19
0
A
MSE
1
n
20
MSE
1
A
ASN
2
n
21
ASN
2
A
LEU
3
n
22
LEU
3
A
VAL
4
n
23
VAL
4
A
GLN
5
n
24
GLN
5
A
ASP
6
n
25
ASP
6
A
LYS
7
n
26
LYS
7
A
VAL
8
n
27
VAL
8
A
THR
9
n
28
THR
9
A
ILE
10
n
29
ILE
10
A
ILE
11
n
30
ILE
11
A
THR
12
n
31
THR
12
A
GLY
13
n
32
GLY
13
A
GLY
14
n
33
GLY
14
A
THR
15
n
34
THR
15
A
ARG
16
n
35
ARG
16
A
GLY
17
n
36
GLY
17
A
ILE
18
n
37
ILE
18
A
GLY
19
n
38
GLY
19
A
PHE
20
n
39
PHE
20
A
ALA
21
n
40
ALA
21
A
ALA
22
n
41
ALA
22
A
ALA
23
n
42
ALA
23
A
LYS
24
n
43
LYS
24
A
ILE
25
n
44
ILE
25
A
PHE
26
n
45
PHE
26
A
ILE
27
n
46
ILE
27
A
ASP
28
n
47
ASP
28
A
ASN
29
n
48
ASN
29
A
GLY
30
n
49
GLY
30
A
ALA
31
n
50
ALA
31
A
LYS
32
n
51
LYS
32
A
VAL
33
n
52
VAL
33
A
SER
34
n
53
SER
34
A
ILE
35
n
54
ILE
35
A
PHE
36
n
55
PHE
36
A
GLY
37
n
56
GLY
37
A
GLU
38
n
57
GLU
38
A
THR
39
n
58
THR
39
A
GLN
40
n
59
GLN
40
A
GLU
41
n
60
GLU
41
A
GLU
42
n
61
GLU
42
A
VAL
43
n
62
VAL
43
A
ASP
44
n
63
ASP
44
A
THR
45
n
64
THR
45
A
ALA
46
n
65
ALA
46
A
LEU
47
n
66
LEU
47
A
ALA
48
n
67
ALA
48
A
GLN
49
n
68
GLN
49
A
LEU
50
n
69
LEU
50
A
LYS
51
n
70
LYS
51
A
GLU
52
n
71
GLU
52
A
LEU
53
n
72
LEU
53
A
TYR
54
n
73
TYR
54
A
PRO
55
n
74
PRO
55
A
GLU
56
n
75
GLU
56
A
GLU
57
n
76
GLU
57
A
GLU
58
n
77
GLU
58
A
VAL
59
n
78
VAL
59
A
LEU
60
n
79
LEU
60
A
GLY
61
n
80
GLY
61
A
PHE
62
n
81
PHE
62
A
ALA
63
n
82
ALA
63
A
PRO
64
n
83
PRO
64
A
ASP
65
n
84
ASP
65
A
LEU
66
n
85
LEU
66
A
THR
67
n
86
THR
67
A
SER
68
n
87
SER
68
A
ARG
69
n
88
ARG
69
A
ASP
70
n
89
ASP
70
A
ALA
71
n
90
ALA
71
A
VAL
72
n
91
VAL
72
A
MSE
73
n
92
MSE
73
A
ALA
74
n
93
ALA
74
A
ALA
75
n
94
ALA
75
A
VAL
76
n
95
VAL
76
A
GLY
77
n
96
GLY
77
A
GLN
78
n
97
GLN
78
A
VAL
79
n
98
VAL
79
A
ALA
80
n
99
ALA
80
A
GLN
81
n
100
GLN
81
A
LYS
82
n
101
LYS
82
A
TYR
83
n
102
TYR
83
A
GLY
84
n
103
GLY
84
A
ARG
85
n
104
ARG
85
A
LEU
86
n
105
LEU
86
A
ASP
87
n
106
ASP
87
A
VAL
88
n
107
VAL
88
A
MSE
89
n
108
MSE
89
A
ILE
90
n
109
ILE
90
A
ASN
91
n
110
ASN
91
A
ASN
92
n
111
ASN
92
A
ALA
93
n
112
ALA
93
A
GLY
94
n
113
GLY
94
A
ILE
95
n
114
ILE
95
A
THR
96
n
115
THR
96
A
SER
97
n
116
SER
97
A
ASN
98
n
117
ASN
98
A
ASN
99
n
118
ASN
99
A
VAL
100
n
119
VAL
100
A
PHE
101
n
120
PHE
101
A
SER
102
n
121
SER
102
A
ARG
103
n
122
ARG
103
A
VAL
104
n
123
VAL
104
A
SER
105
n
124
SER
105
A
GLU
106
n
125
GLU
106
A
GLU
107
n
126
GLU
107
A
GLU
108
n
127
GLU
108
A
PHE
109
n
128
PHE
109
A
LYS
110
n
129
LYS
110
A
HIS
111
n
130
HIS
111
A
ILE
112
n
131
ILE
112
A
MSE
113
n
132
MSE
113
A
ASP
114
n
133
ASP
114
A
ILE
115
n
134
ILE
115
A
ASN
116
n
135
ASN
116
A
VAL
117
n
136
VAL
117
A
THR
118
n
137
THR
118
A
GLY
119
n
138
GLY
119
A
VAL
120
n
139
VAL
120
A
PHE
121
n
140
PHE
121
A
ASN
122
n
141
ASN
122
A
GLY
123
n
142
GLY
123
A
ALA
124
n
143
ALA
124
A
TRP
125
n
144
TRP
125
A
CYS
126
n
145
CYS
126
A
ALA
127
n
146
ALA
127
A
TYR
128
n
147
TYR
128
A
GLN
129
n
148
GLN
129
A
CYS
130
n
149
CYS
130
A
MSE
131
n
150
MSE
131
A
LYS
132
n
151
LYS
132
A
ASP
133
n
152
ASP
133
A
ALA
134
n
153
ALA
134
A
LYS
135
n
154
LYS
135
A
LYS
136
n
155
LYS
136
A
GLY
137
n
156
GLY
137
A
VAL
138
n
157
VAL
138
A
ILE
139
n
158
ILE
139
A
ILE
140
n
159
ILE
140
A
ASN
141
n
160
ASN
141
A
THR
142
n
161
THR
142
A
ALA
143
n
162
ALA
143
A
SER
144
n
163
SER
144
A
VAL
145
n
164
VAL
145
A
THR
146
n
165
THR
146
A
GLY
147
n
166
GLY
147
A
ILE
148
n
167
ILE
148
A
PHE
149
n
168
PHE
149
A
n
169
150
A
n
170
151
A
n
171
152
A
n
172
153
A
n
173
154
A
n
174
155
A
n
175
156
A
n
176
157
A
PRO
158
n
177
PRO
158
A
ALA
159
n
178
ALA
159
A
SER
160
n
179
SER
160
A
LYS
161
n
180
LYS
161
A
ALA
162
n
181
ALA
162
A
SER
163
n
182
SER
163
A
VAL
164
n
183
VAL
164
A
ILE
165
n
184
ILE
165
A
GLY
166
n
185
GLY
166
A
LEU
167
n
186
LEU
167
A
THR
168
n
187
THR
168
A
HIS
169
n
188
HIS
169
A
GLY
170
n
189
GLY
170
A
LEU
171
n
190
LEU
171
A
GLY
172
n
191
GLY
172
A
ARG
173
n
192
ARG
173
A
GLU
174
n
193
GLU
174
A
ILE
175
n
194
ILE
175
A
ILE
176
n
195
ILE
176
A
ARG
177
n
196
ARG
177
A
LYS
178
n
197
LYS
178
A
ASN
179
n
198
ASN
179
A
ILE
180
n
199
ILE
180
A
ARG
181
n
200
ARG
181
A
VAL
182
n
201
VAL
182
A
VAL
183
n
202
VAL
183
A
GLY
184
n
203
GLY
184
A
VAL
185
n
204
VAL
185
A
ALA
186
n
205
ALA
186
A
PRO
187
n
206
PRO
187
A
GLY
188
n
207
GLY
188
A
VAL
189
n
208
VAL
189
A
VAL
190
n
209
VAL
190
A
ASN
191
n
210
ASN
191
A
THR
192
n
211
THR
192
A
n
212
193
A
n
213
194
A
n
214
195
A
n
215
196
A
n
216
197
A
n
217
198
A
n
218
199
A
n
219
200
A
n
220
201
A
n
221
202
A
n
222
203
A
n
223
204
A
n
224
205
A
n
225
206
A
n
226
207
A
n
227
208
A
n
228
209
A
n
229
210
A
n
230
211
A
n
231
212
A
n
232
213
A
n
233
214
A
MSE
215
n
234
MSE
215
A
LEU
216
n
235
LEU
216
A
GLU
217
n
236
GLU
217
A
PRO
218
n
237
PRO
218
A
GLU
219
n
238
GLU
219
A
GLU
220
n
239
GLU
220
A
ILE
221
n
240
ILE
221
A
ALA
222
n
241
ALA
222
A
ASN
223
n
242
ASN
223
A
VAL
224
n
243
VAL
224
A
TYR
225
n
244
TYR
225
A
LEU
226
n
245
LEU
226
A
PHE
227
n
246
PHE
227
A
LEU
228
n
247
LEU
228
A
ALA
229
n
248
ALA
229
A
SER
230
n
249
SER
230
A
ASP
231
n
250
ASP
231
A
LEU
232
n
251
LEU
232
A
ALA
233
n
252
ALA
233
A
SER
234
n
253
SER
234
A
GLY
235
n
254
GLY
235
A
ILE
236
n
255
ILE
236
A
THR
237
n
256
THR
237
A
ALA
238
n
257
ALA
238
A
THR
239
n
258
THR
239
A
THR
240
n
259
THR
240
A
VAL
241
n
260
VAL
241
A
SER
242
n
261
SER
242
A
VAL
243
n
262
VAL
243
A
ASP
244
n
263
ASP
244
A
GLY
245
n
264
GLY
245
A
n
265
246
A
n
266
247
A
n
267
248
A
n
268
249
A
1.1577
0.1051
0.1795
1.1567
-0.2648
1.2810
0.0090
0.0973
-0.0998
-0.0305
-0.0357
-0.0844
0.0582
0.0771
0.0268
0.0714
0.0001
0.0056
0.0788
-0.0148
0.0896
refined
27.1884
63.2670
68.8789
X-RAY DIFFRACTION
A
1
A
245
X-RAY DIFFRACTION
1
author_and_software_defined_assembly
PISA
4
tetrameric
9140
-106
31000
A
MSE
1
SELENOMETHIONINE
A
MSE
20
MET
A
MSE
73
SELENOMETHIONINE
A
MSE
92
MET
A
MSE
89
SELENOMETHIONINE
A
MSE
108
MET
A
MSE
113
SELENOMETHIONINE
A
MSE
132
MET
A
MSE
131
SELENOMETHIONINE
A
MSE
150
MET
A
MSE
215
SELENOMETHIONINE
A
MSE
234
MET
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
54.0410000000
93.1780000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
3_656
-x+1,y,-z+1
crystal symmetry operation
54.0410000000
0.0000000000
105.4430000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_566
x,-y+1,-z+1
crystal symmetry operation
0.0000000000
93.1780000000
105.4430000000
A
O
LEU
60
A
O
LEU
79
A
N
ILE
35
A
N
ILE
54
A
O
LYS
32
A
O
LYS
51
A
N
THR
9
A
N
THR
28
A
N
ILE
10
A
N
ILE
29
A
O
ILE
90
A
O
ILE
109
A
N
ASN
91
A
N
ASN
110
A
O
ILE
140
A
O
ILE
159
A
N
ILE
139
A
N
ILE
158
A
O
ARG
181
A
O
ARG
200
A
N
GLY
184
A
N
GLY
203
A
O
VAL
241
A
O
VAL
260
1
A
CG
LYS
135
A
CG
LYS
154
1
Y
1
A
CD
LYS
135
A
CD
LYS
154
1
Y
1
A
CE
LYS
135
A
CE
LYS
154
1
Y
1
A
NZ
LYS
135
A
NZ
LYS
154
1
Y
1
A
N
PRO
158
A
N
PRO
177
1
Y
1
A
CB
PRO
158
A
CB
PRO
177
1
Y
1
A
CG
PRO
158
A
CG
PRO
177
1
Y
1
A
CD
PRO
158
A
CD
PRO
177
1
Y
1
A
C
GLY
245
A
C
GLY
264
1
Y
1
A
O
GLY
245
A
O
GLY
264
1
Y
1
A
MSE
-18
A
MSE
1
1
Y
1
A
GLY
-17
A
GLY
2
1
Y
1
A
SER
-16
A
SER
3
1
Y
1
A
ASP
-15
A
ASP
4
1
Y
1
A
LYS
-14
A
LYS
5
1
Y
1
A
ILE
-13
A
ILE
6
1
Y
1
A
HIS
-12
A
HIS
7
1
Y
1
A
HIS
-11
A
HIS
8
1
Y
1
A
HIS
-10
A
HIS
9
1
Y
1
A
HIS
-9
A
HIS
10
1
Y
1
A
HIS
-8
A
HIS
11
1
Y
1
A
HIS
-7
A
HIS
12
1
Y
1
A
GLU
-6
A
GLU
13
1
Y
1
A
ASN
-5
A
ASN
14
1
Y
1
A
LEU
-4
A
LEU
15
1
Y
1
A
TYR
-3
A
TYR
16
1
Y
1
A
PHE
-2
A
PHE
17
1
Y
1
A
GLN
-1
A
GLN
18
1
Y
1
A
GLY
0
A
GLY
19
1
Y
1
A
GLY
150
A
GLY
169
1
Y
1
A
SER
151
A
SER
170
1
Y
1
A
LEU
152
A
LEU
171
1
Y
1
A
SER
153
A
SER
172
1
Y
1
A
GLY
154
A
GLY
173
1
Y
1
A
VAL
155
A
VAL
174
1
Y
1
A
GLY
156
A
GLY
175
1
Y
1
A
TYR
157
A
TYR
176
1
Y
1
A
ASP
193
A
ASP
212
1
Y
1
A
MSE
194
A
MSE
213
1
Y
1
A
THR
195
A
THR
214
1
Y
1
A
ASN
196
A
ASN
215
1
Y
1
A
GLY
197
A
GLY
216
1
Y
1
A
ASN
198
A
ASN
217
1
Y
1
A
PRO
199
A
PRO
218
1
Y
1
A
PRO
200
A
PRO
219
1
Y
1
A
GLU
201
A
GLU
220
1
Y
1
A
ILE
202
A
ILE
221
1
Y
1
A
MSE
203
A
MSE
222
1
Y
1
A
GLU
204
A
GLU
223
1
Y
1
A
GLY
205
A
GLY
224
1
Y
1
A
TYR
206
A
TYR
225
1
Y
1
A
LEU
207
A
LEU
226
1
Y
1
A
LYS
208
A
LYS
227
1
Y
1
A
ALA
209
A
ALA
228
1
Y
1
A
LEU
210
A
LEU
229
1
Y
1
A
PRO
211
A
PRO
230
1
Y
1
A
MSE
212
A
MSE
231
1
Y
1
A
LYS
213
A
LYS
232
1
Y
1
A
ARG
214
A
ARG
233
1
Y
1
A
ALA
246
A
ALA
265
1
Y
1
A
TYR
247
A
TYR
266
1
Y
1
A
ARG
248
A
ARG
267
1
Y
1
A
PRO
249
A
PRO
268
1
Y
1
A
A
OE1
O
GLU
HOH
108
445
2.17
B
1
A
PHE
101
-27.02
-60.79
132.190
44.9133
21.460
-0.8700
-0.0000
0.0000
2.6400
0.0000
-1.7700
0.9730
0.9630
1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. CHLORIDE (CL) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED INTO THE STRUCTURE. 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 6. THE SCATTERING FACTORS FOR SULFUR, CHLORINE AND SELENIUM ATOMS WERE ADJUSTED BY REFMAC 5.7.0032 TO ACCOUNT FOR ANOMALOUS DISPERSION BASED ON THE WAVELENGTH 0.91162 A (S f'= 0.16, Cl f'= 0.19, Se f'= -1.81). THE CROMER MANN c VALUES LISTED IN THE CIF VERSION OF THE FILE INCLUDE THIS CORRECTION.
0.1873
0.1616
0.1629
1.9000
29.794
1097
20248
21345
5.1000
99.6300
1.000
0.250
5.4630
0.0760
RANDOM
1
THROUGHOUT
0.000
MAD
0.1140
0.1070
0.8000
0.8000
1.2000
MAXIMUM LIKELIHOOD WITH PHASES
BABINET MODEL WITH MASK
1.9000
29.794
101
1694
1
0
1592
0.011
0.019
1686
0.001
0.020
1671
1.404
1.971
2297
0.729
3.000
3845
5.483
5.000
236
39.260
25.072
69
14.245
15.000
277
14.652
15.000
9
0.070
0.200
278
0.005
0.020
1946
0.001
0.020
367
4.167
5.938
878
4.165
5.941
879
5.652
11.000
1099
5.983
7.094
808
0.2960
0.2910
1.9490
71
1495
1566
20
99.8100
1.90
29.794
4IS2
21347
21347
0.037
0.074
0.063
1
7.675
9.900
78306
3.700
99.900
0.887
0.758
1.900
1.950
1.7
5806
1573
0.452
0.887
0.758
1
1.7
3.7
100.0
0.708
0.606
1.950
2.000
2.0
5592
1505
0.359
0.708
0.606
1
2.0
3.7
100.0
0.535
0.457
2.000
2.060
2.7
5423
1479
0.272
0.535
0.457
1
2.7
3.7
100.0
0.365
0.312
2.060
2.120
3.6
5269
1432
0.186
0.365
0.312
1
3.6
3.7
100.0
0.298
0.255
2.120
2.190
4.4
5170
1409
0.152
0.298
0.255
1
4.4
3.7
100.0
0.237
0.203
2.190
2.270
5.3
5020
1358
0.120
0.237
0.203
1
5.2
3.7
100.0
0.194
0.166
2.270
2.360
6.1
4846
1308
0.099
0.194
0.166
1
6.1
3.7
100.0
0.155
0.133
2.360
2.450
7.2
4644
1261
0.078
0.155
0.133
1
7.2
3.7
100.0
0.136
0.117
2.450
2.560
8.5
4424
1199
0.068
0.136
0.117
1
8.5
3.7
100.0
0.119
0.102
2.560
2.690
10.3
4304
1167
0.059
0.119
0.102
1
10.3
3.7
100.0
0.108
0.093
2.690
2.830
11.4
4032
1097
0.054
0.108
0.093
1
11.4
3.7
100.0
0.091
0.079
2.830
3.000
14.0
3870
1049
0.045
0.091
0.079
1
14.0
3.7
100.0
0.079
0.067
3.000
3.210
15.9
3560
975
0.040
0.079
0.067
1
15.9
3.7
100.0
0.065
0.056
3.210
3.470
19.0
3403
928
0.032
0.065
0.056
1
19.0
3.7
99.9
0.052
0.045
3.470
3.800
21.7
3126
851
0.025
0.052
0.045
1
21.7
3.7
99.9
0.043
0.037
3.800
4.250
23.3
2774
766
0.022
0.043
0.037
1
23.3
3.6
99.7
0.044
0.038
4.250
4.910
24.8
2524
696
0.022
0.044
0.038
1
24.8
3.6
99.8
0.048
0.042
4.910
6.010
23.5
2063
579
0.024
0.048
0.042
1
23.5
3.6
99.5
0.048
0.041
6.010
8.500
23.7
1630
462
0.024
0.048
0.041
1
23.7
3.5
98.9
0.042
0.035
8.500
29.794
25.4
826
253
0.022
0.042
0.035
1
25.4
3.3
93.6
model building
D.C. & J.S. Richardson lab
molprobity@kinemage.biochem.duke.edu
http://kinemage.biochem.duke.edu/molprobity/
MolProbity
package
3beta29
data extraction
PDB
deposit@deposit.rcsb.org
June 10, 2010
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.10
phasing
George M. Sheldrick
gsheldr@shelx.uni-ac.gwdg.de
Fortran_77
http://shelx.uni-ac.gwdg.de/SHELX/
SHELX
package
phasing
Eric de La Fortelle
sharp-develop@globalphasing.com
http://www.globalphasing.com/sharp/
SHARP
package
data scaling
Phil Evans
pre@mrc-lmb.cam.ac.uk
SCALA
package
3.3.15
refinement
Garib N. Murshudov
garib@mrc-lmb.cam.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
5.7.0032
data reduction
MOSFLM
phasing
SHELXD
Y
Crystal structure of the apo form of a 3alpha-hydroxysteroid dehydrogenase (BaiA2) associated with secondary bile acid synthesis from Clostridium scindens VPI12708 at 1.90 A resolution
1
N
N
2
N
N
3
N
N
A
ARG
16
A
ARG
35
HELX_P
A
ASN
29
A
ASN
48
1
1
14
A
THR
39
A
THR
58
HELX_P
A
TYR
54
A
TYR
73
1
2
16
A
SER
68
A
SER
87
HELX_P
A
GLY
84
A
GLY
103
1
3
17
A
VAL
100
A
VAL
119
HELX_P
A
VAL
104
A
VAL
123
5
4
5
A
SER
105
A
SER
124
HELX_P
A
VAL
117
A
VAL
136
1
5
13
A
VAL
117
A
VAL
136
HELX_P
A
LYS
132
A
LYS
151
1
6
16
A
ALA
159
A
ALA
178
HELX_P
A
ILE
175
A
ILE
194
1
7
17
A
ILE
176
A
ILE
195
HELX_P
A
LYS
178
A
LYS
197
5
8
3
A
GLU
217
A
GLU
236
HELX_P
A
SER
230
A
SER
249
1
9
14
A
ASP
231
A
ASP
250
HELX_P
A
SER
234
A
SER
253
5
10
4
covale
1.316
both
A
MSE
1
A
C
MSE
20
1_555
A
ASN
2
A
N
ASN
21
1_555
covale
1.335
both
A
VAL
72
A
C
VAL
91
1_555
A
MSE
73
A
N
MSE
92
1_555
covale
1.316
both
A
MSE
73
A
C
MSE
92
1_555
A
ALA
74
A
N
ALA
93
1_555
covale
1.343
both
A
VAL
88
A
C
VAL
107
1_555
A
MSE
89
A
N
MSE
108
1_555
covale
1.330
both
A
MSE
89
A
C
MSE
108
1_555
A
ILE
90
A
N
ILE
109
1_555
covale
1.326
both
A
ILE
112
A
C
ILE
131
1_555
A
MSE
113
A
N
MSE
132
1_555
covale
1.327
both
A
MSE
113
A
C
MSE
132
1_555
A
ASP
114
A
N
ASP
133
1_555
covale
1.332
both
A
CYS
130
A
C
CYS
149
1_555
A
MSE
131
A
N
MSE
150
1_555
covale
1.327
both
A
MSE
131
A
C
MSE
150
1_555
A
LYS
132
A
N
LYS
151
1_555
covale
1.328
both
A
MSE
215
A
C
MSE
234
1_555
A
LEU
216
A
N
LEU
235
1_555
OXIDOREDUCTASE
NAD(P)-binding Rossmann-fold domains, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, OXIDOREDUCTASE
BAIA2_EUBSP
UNP
1
1
P19337
MNLVQDKVTIITGGTRGIGFAAAKIFIDNGAKVSIFGETQEEVDTALAQLKELYPEEEVLGFAPDLTSRDAVMAAVGQVA
QKYGRLDVMINNAGITSNNVFSRVSEEEFKHIMDINVTGVFNGAWCAYQCMKDAKKGVIINTASVTGIFGSLSGVGYPAS
KASVIGLTHGLGREIIRKNIRVVGVAPGVVNTDMTNGNPPEIMEGYLKALPMKRMLEPEEIANVYLFLASDLASGITATT
VSVDGAYRP
1
249
4IS2
1
249
P19337
A
1
20
268
1
expression tag
MSE
-18
4IS2
A
P19337
UNP
1
1
expression tag
GLY
-17
4IS2
A
P19337
UNP
2
1
expression tag
SER
-16
4IS2
A
P19337
UNP
3
1
expression tag
ASP
-15
4IS2
A
P19337
UNP
4
1
expression tag
LYS
-14
4IS2
A
P19337
UNP
5
1
expression tag
ILE
-13
4IS2
A
P19337
UNP
6
1
expression tag
HIS
-12
4IS2
A
P19337
UNP
7
1
expression tag
HIS
-11
4IS2
A
P19337
UNP
8
1
expression tag
HIS
-10
4IS2
A
P19337
UNP
9
1
expression tag
HIS
-9
4IS2
A
P19337
UNP
10
1
expression tag
HIS
-8
4IS2
A
P19337
UNP
11
1
expression tag
HIS
-7
4IS2
A
P19337
UNP
12
1
expression tag
GLU
-6
4IS2
A
P19337
UNP
13
1
expression tag
ASN
-5
4IS2
A
P19337
UNP
14
1
expression tag
LEU
-4
4IS2
A
P19337
UNP
15
1
expression tag
TYR
-3
4IS2
A
P19337
UNP
16
1
expression tag
PHE
-2
4IS2
A
P19337
UNP
17
1
expression tag
GLN
-1
4IS2
A
P19337
UNP
18
1
expression tag
GLY
0
4IS2
A
P19337
UNP
19
7
parallel
parallel
parallel
parallel
parallel
parallel
A
LEU
60
A
LEU
79
A
PHE
62
A
PHE
81
A
LYS
32
A
LYS
51
A
PHE
36
A
PHE
55
A
VAL
8
A
VAL
27
A
ILE
11
A
ILE
30
A
VAL
88
A
VAL
107
A
ASN
91
A
ASN
110
A
GLY
137
A
GLY
156
A
THR
142
A
THR
161
A
ILE
180
A
ILE
199
A
PRO
187
A
PRO
206
A
THR
239
A
THR
258
A
VAL
243
A
VAL
262
BINDING SITE FOR RESIDUE CL A 301
A
CL
301
Software
3
A
TYR
54
A
TYR
73
3
1_555
A
PRO
55
A
PRO
74
3
1_555
A
GLU
56
A
GLU
75
3
1_555
23
I 2 2 2