0.023050
0.000000
0.000000
0.000000
0.021602
0.000000
0.000000
0.000000
0.009838
0.000000
0.000000
0.000000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
90.000
90.000
43.384
46.292
101.644
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 Se
196.106
n
SELENOMETHIONINE
L-peptide linking
C4 H10 O3
106.120
DI(HYDROXYETHYL)ETHER
non-polymer
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 predicted CIB-like hydrolase (NP_393672.1) from Thermoplasma acidophilum at 1.45 A resolution
10.2210/pdb3bdi/pdb
pdb_00003bdi
100
1
Adjustable focusing mirrors in K-B geometry
CCD
2007-10-25
MARMOSAIC 300 mm CCD
Si(111) Double crystal
MAD
M
x-ray
1
0.94939
1.0
0.97939
1.0
0.97953
1.0
23-ID-D
APS
0.94939, 0.97939, 0.97953
SYNCHROTRON
APS BEAMLINE 23-ID-D
23516.635
Uncharacterized protein Ta0194
1
man
polymer
106.120
DI(HYDROXYETHYL)ETHER
3
syn
non-polymer
18.015
water
203
nat
water
no
yes
G(MSE)ALQEEFIDVNGTRVFQRK(MSE)VTDSNRRSIALFHGYSFTS(MSE)DWDKADLFNNYSKIGYNVYAPDYPGFG
RSASSEKYGIDRGDLKHAAEFIRDYLKANGVARSVI(MSE)GAS(MSE)GGG(MSE)VI(MSE)TTLQYPDIVDGIIAVA
PAWVESLKGD(MSE)KKIRQKTLLVWGSKDHVVPIALSKEYASIISGSRLEIVEGSGHPVYIEKPEEFVRITVDFLRNL
GMALQEEFIDVNGTRVFQRKMVTDSNRRSIALFHGYSFTSMDWDKADLFNNYSKIGYNVYAPDYPGFGRSASSEKYGIDR
GDLKHAAEFIRDYLKANGVARSVIMGASMGGGMVIMTTLQYPDIVDGIIAVAPAWVESLKGDMKKIRQKTLLVWGSKDHV
VPIALSKEYASIISGSRLEIVEGSGHPVYIEKPEEFVRITVDFLRNL
A
388819
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
Thermoplasma
Thermoplasma acidophilum
DSM 1728, AMRC-C165, IFO 15155, JCM 9062
Escherichia
sample
25905
NP_393672.1, Ta0194
273075
Thermoplasma acidophilum DSM 1728
562
Escherichia coli
HK100
Plasmid
speedET
1
2.17
43.32
VAPOR DIFFUSION, SITTING DROP
6.5
NANODROP, 5.0% PEG 3000, 44.0% PEG 400, 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
Joint Center for Structural Genomics
JCSG
PSI, Protein Structure Initiative
software
software
struct_conn
database_2
struct_ref_seq_dif
struct_site
repository
Initial release
Advisory
Version format compliance
Refinement description
Data collection
Derived calculations
Refinement description
Database references
Derived calculations
1
0
2007-11-27
1
1
2011-07-13
1
2
2017-10-25
1
3
2019-07-24
1
4
2023-01-25
_software.classification
_software.name
_software.classification
_software.contact_author
_software.contact_author_email
_software.language
_software.location
_software.name
_software.type
_software.version
_struct_conn.pdbx_leaving_atom_flag
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
SEQUENCE
1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG
MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE
LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
2. DNA SEQUENCING OF THE CLONED CONSTRUCT REVEALS A GLU AT
POSITION 190 INSTEAD OF LYS. THIS IS CONSISTENT WITH THE
OBSERVED ELECTRON DENSITY AT THIS POSITION.
Y
RCSB
Y
RCSB
2007-11-14
REL
REL
PEG
DI(HYDROXYETHYL)ETHER
HOH
water
REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION
REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE
REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
REMARK 999 DNA SEQUENCING OF THE CLONED CONSTRUCT REVEALS A GLU AT POSITION
REMARK 999 190 INSTEAD OF LYS. THIS IS CONSISTENT WITH THE OBSERVED ELECTRON
REMARK 999 DENSITY AT THIS POSITION.
REMARK 999
PEG
1
2
PEG
PEG
207
A
PEG
2
2
PEG
PEG
208
A
PEG
3
2
PEG
PEG
209
A
HOH
4
3
HOH
HOH
210
A
HOH
5
3
HOH
HOH
211
A
HOH
6
3
HOH
HOH
212
A
HOH
7
3
HOH
HOH
213
A
HOH
8
3
HOH
HOH
214
A
HOH
9
3
HOH
HOH
215
A
HOH
10
3
HOH
HOH
216
A
HOH
11
3
HOH
HOH
217
A
HOH
12
3
HOH
HOH
218
A
HOH
13
3
HOH
HOH
219
A
HOH
14
3
HOH
HOH
220
A
HOH
15
3
HOH
HOH
221
A
HOH
16
3
HOH
HOH
222
A
HOH
17
3
HOH
HOH
223
A
HOH
18
3
HOH
HOH
224
A
HOH
19
3
HOH
HOH
225
A
HOH
20
3
HOH
HOH
226
A
HOH
21
3
HOH
HOH
227
A
HOH
22
3
HOH
HOH
228
A
HOH
23
3
HOH
HOH
229
A
HOH
24
3
HOH
HOH
230
A
HOH
25
3
HOH
HOH
231
A
HOH
26
3
HOH
HOH
232
A
HOH
27
3
HOH
HOH
233
A
HOH
28
3
HOH
HOH
234
A
HOH
29
3
HOH
HOH
235
A
HOH
30
3
HOH
HOH
236
A
HOH
31
3
HOH
HOH
237
A
HOH
32
3
HOH
HOH
238
A
HOH
33
3
HOH
HOH
239
A
HOH
34
3
HOH
HOH
240
A
HOH
35
3
HOH
HOH
241
A
HOH
36
3
HOH
HOH
242
A
HOH
37
3
HOH
HOH
243
A
HOH
38
3
HOH
HOH
244
A
HOH
39
3
HOH
HOH
245
A
HOH
40
3
HOH
HOH
246
A
HOH
41
3
HOH
HOH
247
A
HOH
42
3
HOH
HOH
248
A
HOH
43
3
HOH
HOH
249
A
HOH
44
3
HOH
HOH
250
A
HOH
45
3
HOH
HOH
251
A
HOH
46
3
HOH
HOH
252
A
HOH
47
3
HOH
HOH
253
A
HOH
48
3
HOH
HOH
254
A
HOH
49
3
HOH
HOH
255
A
HOH
50
3
HOH
HOH
256
A
HOH
51
3
HOH
HOH
257
A
HOH
52
3
HOH
HOH
258
A
HOH
53
3
HOH
HOH
259
A
HOH
54
3
HOH
HOH
260
A
HOH
55
3
HOH
HOH
261
A
HOH
56
3
HOH
HOH
262
A
HOH
57
3
HOH
HOH
263
A
HOH
58
3
HOH
HOH
264
A
HOH
59
3
HOH
HOH
265
A
HOH
60
3
HOH
HOH
266
A
HOH
61
3
HOH
HOH
267
A
HOH
62
3
HOH
HOH
268
A
HOH
63
3
HOH
HOH
269
A
HOH
64
3
HOH
HOH
270
A
HOH
65
3
HOH
HOH
271
A
HOH
66
3
HOH
HOH
272
A
HOH
67
3
HOH
HOH
273
A
HOH
68
3
HOH
HOH
274
A
HOH
69
3
HOH
HOH
275
A
HOH
70
3
HOH
HOH
276
A
HOH
71
3
HOH
HOH
277
A
HOH
72
3
HOH
HOH
278
A
HOH
73
3
HOH
HOH
279
A
HOH
74
3
HOH
HOH
280
A
HOH
75
3
HOH
HOH
281
A
HOH
76
3
HOH
HOH
282
A
HOH
77
3
HOH
HOH
283
A
HOH
78
3
HOH
HOH
284
A
HOH
79
3
HOH
HOH
285
A
HOH
80
3
HOH
HOH
286
A
HOH
81
3
HOH
HOH
287
A
HOH
82
3
HOH
HOH
288
A
HOH
83
3
HOH
HOH
289
A
HOH
84
3
HOH
HOH
290
A
HOH
85
3
HOH
HOH
291
A
HOH
86
3
HOH
HOH
292
A
HOH
87
3
HOH
HOH
293
A
HOH
88
3
HOH
HOH
294
A
HOH
89
3
HOH
HOH
295
A
HOH
90
3
HOH
HOH
296
A
HOH
91
3
HOH
HOH
297
A
HOH
92
3
HOH
HOH
298
A
HOH
93
3
HOH
HOH
299
A
HOH
94
3
HOH
HOH
300
A
HOH
95
3
HOH
HOH
301
A
HOH
96
3
HOH
HOH
302
A
HOH
97
3
HOH
HOH
303
A
HOH
98
3
HOH
HOH
304
A
HOH
99
3
HOH
HOH
305
A
HOH
100
3
HOH
HOH
306
A
HOH
101
3
HOH
HOH
307
A
HOH
102
3
HOH
HOH
308
A
HOH
103
3
HOH
HOH
309
A
HOH
104
3
HOH
HOH
310
A
HOH
105
3
HOH
HOH
311
A
HOH
106
3
HOH
HOH
312
A
HOH
107
3
HOH
HOH
313
A
HOH
108
3
HOH
HOH
314
A
HOH
109
3
HOH
HOH
315
A
HOH
110
3
HOH
HOH
316
A
HOH
111
3
HOH
HOH
317
A
HOH
112
3
HOH
HOH
318
A
HOH
113
3
HOH
HOH
319
A
HOH
114
3
HOH
HOH
320
A
HOH
115
3
HOH
HOH
321
A
HOH
116
3
HOH
HOH
322
A
HOH
117
3
HOH
HOH
323
A
HOH
118
3
HOH
HOH
324
A
HOH
119
3
HOH
HOH
325
A
HOH
120
3
HOH
HOH
326
A
HOH
121
3
HOH
HOH
327
A
HOH
122
3
HOH
HOH
328
A
HOH
123
3
HOH
HOH
329
A
HOH
124
3
HOH
HOH
330
A
HOH
125
3
HOH
HOH
331
A
HOH
126
3
HOH
HOH
332
A
HOH
127
3
HOH
HOH
333
A
HOH
128
3
HOH
HOH
334
A
HOH
129
3
HOH
HOH
335
A
HOH
130
3
HOH
HOH
336
A
HOH
131
3
HOH
HOH
337
A
HOH
132
3
HOH
HOH
338
A
HOH
133
3
HOH
HOH
339
A
HOH
134
3
HOH
HOH
340
A
HOH
135
3
HOH
HOH
341
A
HOH
136
3
HOH
HOH
342
A
HOH
137
3
HOH
HOH
343
A
HOH
138
3
HOH
HOH
344
A
HOH
139
3
HOH
HOH
345
A
HOH
140
3
HOH
HOH
346
A
HOH
141
3
HOH
HOH
347
A
HOH
142
3
HOH
HOH
348
A
HOH
143
3
HOH
HOH
349
A
HOH
144
3
HOH
HOH
350
A
HOH
145
3
HOH
HOH
351
A
HOH
146
3
HOH
HOH
352
A
HOH
147
3
HOH
HOH
353
A
HOH
148
3
HOH
HOH
354
A
HOH
149
3
HOH
HOH
355
A
HOH
150
3
HOH
HOH
356
A
HOH
151
3
HOH
HOH
357
A
HOH
152
3
HOH
HOH
358
A
HOH
153
3
HOH
HOH
359
A
HOH
154
3
HOH
HOH
360
A
HOH
155
3
HOH
HOH
361
A
HOH
156
3
HOH
HOH
362
A
HOH
157
3
HOH
HOH
363
A
HOH
158
3
HOH
HOH
364
A
HOH
159
3
HOH
HOH
365
A
HOH
160
3
HOH
HOH
366
A
HOH
161
3
HOH
HOH
367
A
HOH
162
3
HOH
HOH
368
A
HOH
163
3
HOH
HOH
369
A
HOH
164
3
HOH
HOH
370
A
HOH
165
3
HOH
HOH
371
A
HOH
166
3
HOH
HOH
372
A
HOH
167
3
HOH
HOH
373
A
HOH
168
3
HOH
HOH
374
A
HOH
169
3
HOH
HOH
375
A
HOH
170
3
HOH
HOH
376
A
HOH
171
3
HOH
HOH
377
A
HOH
172
3
HOH
HOH
378
A
HOH
173
3
HOH
HOH
379
A
HOH
174
3
HOH
HOH
380
A
HOH
175
3
HOH
HOH
381
A
HOH
176
3
HOH
HOH
382
A
HOH
177
3
HOH
HOH
383
A
HOH
178
3
HOH
HOH
384
A
HOH
179
3
HOH
HOH
385
A
HOH
180
3
HOH
HOH
386
A
HOH
181
3
HOH
HOH
387
A
HOH
182
3
HOH
HOH
388
A
HOH
183
3
HOH
HOH
389
A
HOH
184
3
HOH
HOH
390
A
HOH
185
3
HOH
HOH
391
A
HOH
186
3
HOH
HOH
392
A
HOH
187
3
HOH
HOH
393
A
HOH
188
3
HOH
HOH
394
A
HOH
189
3
HOH
HOH
395
A
HOH
190
3
HOH
HOH
396
A
HOH
191
3
HOH
HOH
397
A
HOH
192
3
HOH
HOH
398
A
HOH
193
3
HOH
HOH
399
A
HOH
194
3
HOH
HOH
400
A
HOH
195
3
HOH
HOH
401
A
HOH
196
3
HOH
HOH
402
A
HOH
197
3
HOH
HOH
403
A
HOH
198
3
HOH
HOH
404
A
HOH
199
3
HOH
HOH
405
A
HOH
200
3
HOH
HOH
406
A
HOH
201
3
HOH
HOH
407
A
HOH
202
3
HOH
HOH
408
A
HOH
203
3
HOH
HOH
409
A
HOH
204
3
HOH
HOH
410
A
HOH
205
3
HOH
HOH
411
A
HOH
206
3
HOH
HOH
412
A
GLY
0
n
1
GLY
0
A
MSE
1
n
2
MSE
1
A
ALA
2
n
3
ALA
2
A
LEU
3
n
4
LEU
3
A
GLN
4
n
5
GLN
4
A
GLU
5
n
6
GLU
5
A
GLU
6
n
7
GLU
6
A
PHE
7
n
8
PHE
7
A
ILE
8
n
9
ILE
8
A
ASP
9
n
10
ASP
9
A
VAL
10
n
11
VAL
10
A
ASN
11
n
12
ASN
11
A
GLY
12
n
13
GLY
12
A
THR
13
n
14
THR
13
A
ARG
14
n
15
ARG
14
A
VAL
15
n
16
VAL
15
A
PHE
16
n
17
PHE
16
A
GLN
17
n
18
GLN
17
A
ARG
18
n
19
ARG
18
A
LYS
19
n
20
LYS
19
A
MSE
20
n
21
MSE
20
A
VAL
21
n
22
VAL
21
A
THR
22
n
23
THR
22
A
ASP
23
n
24
ASP
23
A
SER
24
n
25
SER
24
A
ASN
25
n
26
ASN
25
A
ARG
26
n
27
ARG
26
A
ARG
27
n
28
ARG
27
A
SER
28
n
29
SER
28
A
ILE
29
n
30
ILE
29
A
ALA
30
n
31
ALA
30
A
LEU
31
n
32
LEU
31
A
PHE
32
n
33
PHE
32
A
HIS
33
n
34
HIS
33
A
GLY
34
n
35
GLY
34
A
TYR
35
n
36
TYR
35
A
SER
36
n
37
SER
36
A
PHE
37
n
38
PHE
37
A
THR
38
n
39
THR
38
A
SER
39
n
40
SER
39
A
MSE
40
n
41
MSE
40
A
ASP
41
n
42
ASP
41
A
TRP
42
n
43
TRP
42
A
ASP
43
n
44
ASP
43
A
LYS
44
n
45
LYS
44
A
ALA
45
n
46
ALA
45
A
ASP
46
n
47
ASP
46
A
LEU
47
n
48
LEU
47
A
PHE
48
n
49
PHE
48
A
ASN
49
n
50
ASN
49
A
ASN
50
n
51
ASN
50
A
TYR
51
n
52
TYR
51
A
SER
52
n
53
SER
52
A
LYS
53
n
54
LYS
53
A
ILE
54
n
55
ILE
54
A
GLY
55
n
56
GLY
55
A
TYR
56
n
57
TYR
56
A
ASN
57
n
58
ASN
57
A
VAL
58
n
59
VAL
58
A
TYR
59
n
60
TYR
59
A
ALA
60
n
61
ALA
60
A
PRO
61
n
62
PRO
61
A
ASP
62
n
63
ASP
62
A
TYR
63
n
64
TYR
63
A
PRO
64
n
65
PRO
64
A
GLY
65
n
66
GLY
65
A
PHE
66
n
67
PHE
66
A
GLY
67
n
68
GLY
67
A
ARG
68
n
69
ARG
68
A
SER
69
n
70
SER
69
A
ALA
70
n
71
ALA
70
A
SER
71
n
72
SER
71
A
SER
72
n
73
SER
72
A
GLU
73
n
74
GLU
73
A
LYS
74
n
75
LYS
74
A
TYR
75
n
76
TYR
75
A
GLY
76
n
77
GLY
76
A
ILE
77
n
78
ILE
77
A
ASP
78
n
79
ASP
78
A
ARG
79
n
80
ARG
79
A
GLY
80
n
81
GLY
80
A
ASP
81
n
82
ASP
81
A
LEU
82
n
83
LEU
82
A
LYS
83
n
84
LYS
83
A
HIS
84
n
85
HIS
84
A
ALA
85
n
86
ALA
85
A
ALA
86
n
87
ALA
86
A
GLU
87
n
88
GLU
87
A
PHE
88
n
89
PHE
88
A
ILE
89
n
90
ILE
89
A
ARG
90
n
91
ARG
90
A
ASP
91
n
92
ASP
91
A
TYR
92
n
93
TYR
92
A
LEU
93
n
94
LEU
93
A
LYS
94
n
95
LYS
94
A
ALA
95
n
96
ALA
95
A
ASN
96
n
97
ASN
96
A
GLY
97
n
98
GLY
97
A
VAL
98
n
99
VAL
98
A
ALA
99
n
100
ALA
99
A
ARG
100
n
101
ARG
100
A
SER
101
n
102
SER
101
A
VAL
102
n
103
VAL
102
A
ILE
103
n
104
ILE
103
A
MSE
104
n
105
MSE
104
A
GLY
105
n
106
GLY
105
A
ALA
106
n
107
ALA
106
A
SER
107
n
108
SER
107
A
MSE
108
n
109
MSE
108
A
GLY
109
n
110
GLY
109
A
GLY
110
n
111
GLY
110
A
GLY
111
n
112
GLY
111
A
MSE
112
n
113
MSE
112
A
VAL
113
n
114
VAL
113
A
ILE
114
n
115
ILE
114
A
MSE
115
n
116
MSE
115
A
THR
116
n
117
THR
116
A
THR
117
n
118
THR
117
A
LEU
118
n
119
LEU
118
A
GLN
119
n
120
GLN
119
A
TYR
120
n
121
TYR
120
A
PRO
121
n
122
PRO
121
A
ASP
122
n
123
ASP
122
A
ILE
123
n
124
ILE
123
A
VAL
124
n
125
VAL
124
A
ASP
125
n
126
ASP
125
A
GLY
126
n
127
GLY
126
A
ILE
127
n
128
ILE
127
A
ILE
128
n
129
ILE
128
A
ALA
129
n
130
ALA
129
A
VAL
130
n
131
VAL
130
A
ALA
131
n
132
ALA
131
A
PRO
132
n
133
PRO
132
A
ALA
133
n
134
ALA
133
A
TRP
134
n
135
TRP
134
A
VAL
135
n
136
VAL
135
A
GLU
136
n
137
GLU
136
A
SER
137
n
138
SER
137
A
LEU
138
n
139
LEU
138
A
LYS
139
n
140
LYS
139
A
GLY
140
n
141
GLY
140
A
ASP
141
n
142
ASP
141
A
MSE
142
n
143
MSE
142
A
LYS
143
n
144
LYS
143
A
LYS
144
n
145
LYS
144
A
ILE
145
n
146
ILE
145
A
ARG
146
n
147
ARG
146
A
GLN
147
n
148
GLN
147
A
LYS
148
n
149
LYS
148
A
THR
149
n
150
THR
149
A
LEU
150
n
151
LEU
150
A
LEU
151
n
152
LEU
151
A
VAL
152
n
153
VAL
152
A
TRP
153
n
154
TRP
153
A
GLY
154
n
155
GLY
154
A
SER
155
n
156
SER
155
A
LYS
156
n
157
LYS
156
A
ASP
157
n
158
ASP
157
A
HIS
158
n
159
HIS
158
A
VAL
159
n
160
VAL
159
A
VAL
160
n
161
VAL
160
A
PRO
161
n
162
PRO
161
A
ILE
162
n
163
ILE
162
A
ALA
163
n
164
ALA
163
A
LEU
164
n
165
LEU
164
A
SER
165
n
166
SER
165
A
LYS
166
n
167
LYS
166
A
GLU
167
n
168
GLU
167
A
TYR
168
n
169
TYR
168
A
ALA
169
n
170
ALA
169
A
SER
170
n
171
SER
170
A
ILE
171
n
172
ILE
171
A
ILE
172
n
173
ILE
172
A
SER
173
n
174
SER
173
A
GLY
174
n
175
GLY
174
A
SER
175
n
176
SER
175
A
ARG
176
n
177
ARG
176
A
LEU
177
n
178
LEU
177
A
GLU
178
n
179
GLU
178
A
ILE
179
n
180
ILE
179
A
VAL
180
n
181
VAL
180
A
GLU
181
n
182
GLU
181
A
GLY
182
n
183
GLY
182
A
SER
183
n
184
SER
183
A
GLY
184
n
185
GLY
184
A
HIS
185
n
186
HIS
185
A
PRO
186
n
187
PRO
186
A
VAL
187
n
188
VAL
187
A
TYR
188
n
189
TYR
188
A
ILE
189
n
190
ILE
189
A
GLU
190
n
191
GLU
190
A
LYS
191
n
192
LYS
191
A
PRO
192
n
193
PRO
192
A
GLU
193
n
194
GLU
193
A
GLU
194
n
195
GLU
194
A
PHE
195
n
196
PHE
195
A
VAL
196
n
197
VAL
196
A
ARG
197
n
198
ARG
197
A
ILE
198
n
199
ILE
198
A
THR
199
n
200
THR
199
A
VAL
200
n
201
VAL
200
A
ASP
201
n
202
ASP
201
A
PHE
202
n
203
PHE
202
A
LEU
203
n
204
LEU
203
A
ARG
204
n
205
ARG
204
A
ASN
205
n
206
ASN
205
A
LEU
206
n
207
LEU
206
A
0.2299
0.1697
-0.0316
0.4640
-0.1047
0.1473
-0.0213
-0.0236
-0.0248
-0.1118
0.0053
-0.0359
-0.0081
0.0068
0.0161
-0.0013
-0.0016
0.0182
-0.0114
0.0010
-0.0160
refined
29.5682
26.7390
13.5602
X-RAY DIFFRACTION
A
0
A
1
A
206
A
207
X-RAY DIFFRACTION
1
software_defined_assembly
PISA
1
monomeric
A
MSE
1
SELENOMETHIONINE
A
MSE
2
MET
A
MSE
20
SELENOMETHIONINE
A
MSE
21
MET
A
MSE
40
SELENOMETHIONINE
A
MSE
41
MET
A
MSE
104
SELENOMETHIONINE
A
MSE
105
MET
A
MSE
108
SELENOMETHIONINE
A
MSE
109
MET
A
MSE
112
SELENOMETHIONINE
A
MSE
113
MET
A
MSE
115
SELENOMETHIONINE
A
MSE
116
MET
A
MSE
142
SELENOMETHIONINE
A
MSE
143
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
A
N
GLU
6
A
N
GLU
7
A
O
GLN
17
A
O
GLN
18
A
N
MSE
20
A
N
MSE
21
A
O
VAL
58
A
O
VAL
59
A
O
ASN
57
A
O
ASN
58
A
N
ARG
27
A
N
ARG
28
A
N
SER
28
A
N
SER
29
A
O
VAL
102
A
O
VAL
103
A
N
GLY
105
A
N
GLY
106
A
O
VAL
130
A
O
VAL
131
A
N
ALA
129
A
N
ALA
130
A
O
LEU
150
A
O
LEU
151
A
N
LEU
151
A
N
LEU
152
A
O
ARG
176
A
O
ARG
177
1
A
CG
ASP
23
A
CG
ASP
24
1
Y
1
A
OD1
ASP
23
A
OD1
ASP
24
1
Y
1
A
OD2
ASP
23
A
OD2
ASP
24
1
Y
1
A
CD
ARG
26
A
CD
ARG
27
1
Y
1
A
NE
ARG
26
A
NE
ARG
27
1
Y
1
A
CZ
ARG
26
A
CZ
ARG
27
1
Y
1
A
NH1
ARG
26
A
NH1
ARG
27
1
Y
1
A
NH2
ARG
26
A
NH2
ARG
27
1
Y
1
A
CZ
ARG
27
A
CZ
ARG
28
1
Y
1
A
NH1
ARG
27
A
NH1
ARG
28
1
Y
1
A
NH2
ARG
27
A
NH2
ARG
28
1
Y
1
A
CE
LYS
83
A
CE
LYS
84
1
Y
1
A
NZ
LYS
83
A
NZ
LYS
84
1
Y
1
A
CE
LYS
94
A
CE
LYS
95
1
Y
1
A
NZ
LYS
94
A
NZ
LYS
95
1
Y
1
A
CD
ARG
100
A
CD
ARG
101
1
Y
1
A
NE
ARG
100
A
NE
ARG
101
1
Y
1
A
CZ
ARG
100
A
CZ
ARG
101
1
Y
1
A
NH1
ARG
100
A
NH1
ARG
101
1
Y
1
A
NH2
ARG
100
A
NH2
ARG
101
1
Y
1
A
CG
LYS
144
A
CG
LYS
145
1
Y
1
A
CD
LYS
144
A
CD
LYS
145
1
Y
1
A
CE
LYS
144
A
CE
LYS
145
1
Y
1
A
NZ
LYS
144
A
NZ
LYS
145
1
Y
1
A
NH1
ARG
146
A
NH1
ARG
147
1
Y
1
A
NH2
ARG
146
A
NH2
ARG
147
1
Y
1
A
CD
LYS
166
A
CD
LYS
167
1
Y
1
A
CE
LYS
166
A
CE
LYS
167
1
Y
1
A
NZ
LYS
166
A
NZ
LYS
167
1
Y
1
A
CD
GLU
193
A
CD
GLU
194
1
Y
1
A
OE1
GLU
193
A
OE1
GLU
194
1
Y
1
A
OE2
GLU
193
A
OE2
GLU
194
1
Y
1
A
A
OE1
O
GLU
HOH
87
318
2.14
B
1
A
A
OE2
OH
GLU
TYR
87
120
2.18
A
1
A
A
CD
OE2
GLU
GLU
178
178
-0.081
0.011
1.252
1.171
A
A
N
1
A
SER
107
62.67
-122.66
1
A
SER
107
62.67
-119.55
11.878
0.780
0.000
0.000
-0.640
0.000
-0.140
0.966
0.951
1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
3. 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
TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL
S-MET INCORPORATION.
4. POLYETHYLENE GLYCOL MOLECULES FROM THE CRYSTALLIZATION
CONDITIONS WERE MODELED.
0.189
0.163
0.164
1.450
27.338
1851
37039
5.000
99.880
2.094
0.041
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
0.00
MAD
0.064
0.066
0.800
0.800
1.200
MAXIMUM LIKELIHOOD WITH PHASES
MASK
1.450
27.338
203
1820
21
0
1596
0.016
0.022
1779
0.001
0.020
1211
1.622
1.956
2414
0.973
3.000
2953
6.481
5.000
232
40.007
23.867
75
12.771
15.000
301
12.993
15.000
11
0.102
0.200
260
0.008
0.020
2038
0.002
0.020
373
0.221
0.200
366
0.196
0.200
1255
0.185
0.200
878
0.086
0.200
895
0.219
0.200
154
0.145
0.200
8
0.292
0.200
67
0.115
0.200
22
1.847
3.000
1191
0.478
3.000
453
2.415
5.000
1795
3.791
7.000
752
4.910
9.000
619
0.267
0.196
1.488
127
2548
2675
20
99.780
12.90
1.45
27.338
3BDI
37089
0.087
0.087
1
3.100
3.500
99.900
0.194
1.45
1.49
3.5
6659
2676
0.194
1
2.50
99.90
0.190
1.49
1.53
3.7
8367
2614
0.190
1
3.20
100.00
0.170
1.53
1.57
4.1
9280
2580
0.170
1
3.60
100.00
0.143
1.57
1.62
4.7
9007
2499
0.143
1
3.60
100.00
0.130
1.62
1.67
5.2
8776
2430
0.130
1
3.60
100.00
0.121
1.67
1.73
5.5
8416
2327
0.121
1
3.60
100.00
0.112
1.73
1.80
5.7
8194
2256
0.112
1
3.60
100.00
0.106
1.80
1.87
6.1
7941
2196
0.106
1
3.60
100.00
0.106
1.87
1.96
6.1
7503
2076
0.106
1
3.60
100.00
0.097
1.96
2.05
6.4
7380
2039
0.097
1
3.60
100.00
0.081
2.05
2.16
7.6
6853
1897
0.081
1
3.60
100.00
0.079
2.16
2.29
8.1
6637
1836
0.079
1
3.60
100.00
0.082
2.29
2.45
7.4
6222
1717
0.082
1
3.60
100.00
0.094
2.45
2.65
6.2
5662
1587
0.094
1
3.60
100.00
0.088
2.65
2.90
5.1
5340
1506
0.088
1
3.50
100.00
0.077
2.90
3.24
7.1
4720
1330
0.077
1
3.50
100.00
0.072
3.24
3.74
6.4
4275
1209
0.072
1
3.50
100.00
0.078
3.74
4.59
5.6
3641
1034
0.078
1
3.50
99.90
0.085
4.59
6.48
5.0
2745
808
0.085
1
3.40
99.40
0.096
6.48
27.338
4.6
1474
472
0.096
1
3.10
96.90
refinement
Murshudov, G.N.
ccp4@dl.ac.uk
Fortran_77
http://www.ccp4.ac.uk/main.html
REFMAC
program
5.2.0019
refinement
P.D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
phasing
Tom Terwilliger
terwilliger@LANL.gov
http://www.solve.lanl.gov/
SOLVE
package
model building
D.C. & J.S. Richardson lab
molprobity@kinemage.biochem.duke.edu
http://kinemage.biochem.duke.edu/molprobity/
MolProbity
package
3beta29
data scaling
Phil Evans
pre@mrc-lmb.cam.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/INDEX.html
SCALA
other
data extraction
PDB
sw-help@rcsb.rutgers.edu
July 2, 2007
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
3.000
data collection
MAR345
CCD
data reduction
MOSFLM
Crystal structure of predicted CIB-like hydrolase (NP_393672.1) from Thermoplasma acidophilum at 1.45 A resolution
1
N
N
2
N
N
2
N
N
2
N
N
3
N
N
A
THR
38
A
THR
39
HELX_P
A
ALA
45
A
ALA
46
5
1
8
A
ASP
46
A
ASP
47
HELX_P
A
LYS
53
A
LYS
54
1
2
8
A
ASP
81
A
ASP
82
HELX_P
A
ASN
96
A
ASN
97
1
3
16
A
SER
107
A
SER
108
HELX_P
A
TYR
120
A
TYR
121
1
4
14
A
VAL
135
A
VAL
136
HELX_P
A
SER
137
A
SER
138
5
5
3
A
LEU
138
A
LEU
139
HELX_P
A
LYS
143
A
LYS
144
1
6
6
A
PRO
161
A
PRO
162
HELX_P
A
ILE
172
A
ILE
173
1
7
12
A
PRO
186
A
PRO
187
HELX_P
A
LYS
191
A
LYS
192
1
8
6
A
LYS
191
A
LYS
192
HELX_P
A
ASN
205
A
ASN
206
1
9
15
covale
1.340
both
A
GLY
0
A
C
GLY
1
1_555
A
MSE
1
A
N
MSE
2
1_555
covale
1.333
both
A
MSE
1
A
C
MSE
2
1_555
A
ALA
2
A
N
ALA
3
1_555
covale
1.327
both
A
LYS
19
A
C
LYS
20
1_555
A
MSE
20
A
N
MSE
21
1_555
covale
1.321
both
A
MSE
20
A
C
MSE
21
1_555
A
VAL
21
A
N
VAL
22
1_555
covale
1.340
both
A
SER
39
A
C
SER
40
1_555
A
MSE
40
A
N
MSE
41
1_555
covale
1.327
both
A
MSE
40
A
C
MSE
41
1_555
A
ASP
41
A
N
ASP
42
1_555
covale
1.325
both
A
A
ILE
103
A
C
ILE
104
1_555
A
MSE
104
A
N
MSE
105
1_555
covale
1.333
both
B
A
ILE
103
A
C
ILE
104
1_555
A
MSE
104
A
N
MSE
105
1_555
covale
1.326
both
A
A
MSE
104
A
C
MSE
105
1_555
A
GLY
105
A
N
GLY
106
1_555
covale
1.334
both
B
A
MSE
104
A
C
MSE
105
1_555
A
GLY
105
A
N
GLY
106
1_555
covale
1.329
both
A
A
SER
107
A
C
SER
108
1_555
A
MSE
108
A
N
MSE
109
1_555
covale
1.342
both
B
A
SER
107
A
C
SER
108
1_555
A
MSE
108
A
N
MSE
109
1_555
covale
1.342
both
A
A
MSE
108
A
C
MSE
109
1_555
A
GLY
109
A
N
GLY
110
1_555
covale
1.331
both
B
A
MSE
108
A
C
MSE
109
1_555
A
GLY
109
A
N
GLY
110
1_555
covale
1.328
both
A
GLY
111
A
C
GLY
112
1_555
A
MSE
112
A
N
MSE
113
1_555
covale
1.342
both
A
MSE
112
A
C
MSE
113
1_555
A
VAL
113
A
N
VAL
114
1_555
covale
1.324
both
A
ILE
114
A
C
ILE
115
1_555
A
MSE
115
A
N
MSE
116
1_555
covale
1.319
both
A
MSE
115
A
C
MSE
116
1_555
A
THR
116
A
N
THR
117
1_555
covale
1.330
both
A
ASP
141
A
C
ASP
142
1_555
A
MSE
142
A
N
MSE
143
1_555
covale
1.346
both
A
MSE
142
A
C
MSE
143
1_555
A
LYS
143
A
N
LYS
144
1_555
HYDROLASE
NP_393672.1, predicted CIB-like hydrolase, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, HYDROLASE
Q9HLN3_THEAC
UNP
1
2
Q9HLN3
NGTRVFQRKMVTDSNRRSIALFHGYSFTSMDWDKADLFNNYSKIGYNVYAPDYPGFGRSASSEKYGIDRGDLKHAAEFIR
DYLKANGVARSVIMGASMGGGMVIMTTLQYPDIVDGIIAVAPAWVESLKGDMKKIRQKTLLVWGSKDHVVPIALSKEYAS
IISGSRLEIVEGSGHPVYIKKPEEFVRITVDFLRNL
2
197
3BDI
11
206
Q9HLN3
A
1
12
207
1
expression tag
GLY
0
3BDI
A
Q9HLN3
UNP
1
1
variant
MSE
1
3BDI
A
Q9HLN3
UNP
2
1
variant
ALA
2
3BDI
A
Q9HLN3
UNP
3
1
variant
LEU
3
3BDI
A
Q9HLN3
UNP
4
1
variant
GLN
4
3BDI
A
Q9HLN3
UNP
5
1
variant
GLU
5
3BDI
A
Q9HLN3
UNP
6
1
variant
GLU
6
3BDI
A
Q9HLN3
UNP
7
1
variant
PHE
7
3BDI
A
Q9HLN3
UNP
8
1
variant
ILE
8
3BDI
A
Q9HLN3
UNP
9
1
variant
ASP
9
3BDI
A
Q9HLN3
UNP
10
1
variant
VAL
10
3BDI
A
Q9HLN3
UNP
11
1
LYS
SEE REMARK 999
GLU
190
3BDI
A
Q9HLN3
UNP
181
191
8
anti-parallel
anti-parallel
parallel
parallel
parallel
parallel
parallel
A
GLN
4
A
GLN
5
A
VAL
10
A
VAL
11
A
THR
13
A
THR
14
A
MSE
20
A
MSE
21
A
TYR
56
A
TYR
57
A
PRO
61
A
PRO
62
A
ARG
27
A
ARG
28
A
PHE
32
A
PHE
33
A
SER
101
A
SER
102
A
ALA
106
A
ALA
107
A
VAL
124
A
VAL
125
A
VAL
130
A
VAL
131
A
THR
149
A
THR
150
A
GLY
154
A
GLY
155
A
ARG
176
A
ARG
177
A
VAL
180
A
VAL
181
BINDING SITE FOR RESIDUE PEG A 207
A
PEG
207
Software
2
BINDING SITE FOR RESIDUE PEG A 208
A
PEG
208
Software
2
BINDING SITE FOR RESIDUE PEG A 209
A
PEG
209
Software
6
A
ASN
11
A
ASN
12
2
1_555
A
LYS
74
A
LYS
75
2
1_555
A
TYR
35
A
TYR
36
2
1_555
A
GLY
65
A
GLY
66
2
1_555
A
GLY
67
A
GLY
68
6
3_655
A
ARG
68
A
ARG
69
6
3_655
A
GLU
190
A
GLU
191
6
1_555
A
LYS
191
A
LYS
192
6
1_555
A
HOH
366
E
HOH
6
1_565
A
HOH
397
E
HOH
6
1_565
19
P 21 21 21