0.014869
0.000000
0.007678
0.000000
0.013437
0.000000
0.000000
0.000000
0.015805
0.00000
0.00000
0.00000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.000
117.310
90.000
67.254
74.421
71.206
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
C2 H6 O2
62.068
1,2-ETHANEDIOL
ETHYLENE GLYCOL
non-polymer
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
O4 S -2
96.063
SULFATE ION
non-polymer
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
To be published
0353
Crystal structure of a hypothetical protein (BACOVA_05496) from Bacteroides ovatus ATCC 8483 at 2.15 A resolution
10.2210/pdb4id2/pdb
pdb_00004id2
100
1
KOHZU: Double Crystal Si(111)
CCD
2012-10-18
ADSC QUANTUM 315
Double Crystal Si(111)
MAD
M
x-ray
1
0.918401
1.0
0.979485
1.0
0.979268
1.0
8.2.2
ALS
0.918401, 0.979485, 0.979268
SYNCHROTRON
ALS BEAMLINE 8.2.2
18471.895
Uncharacterized protein
2
man
polymer
96.063
SULFATE ION
1
syn
non-polymer
62.068
1,2-ETHANEDIOL
2
syn
non-polymer
18.015
water
109
nat
water
no
yes
GCGGKKGSSDNTSTLA(MSE)IDSVDAHGLQR(MSE)QTSKSETDFKFKGKDYHSLVSRTPDDNLPHVTNELGDTYVDNK
IVLHLTRGNETVLNKTFTKNDFSSVVDANFLSKSILEGIVYDKTTPQGIVYAASVCYPQTDLY(MSE)PLSITITADGK
(MSE)SIQKVDILEEDYDDEAPN
GCGGKKGSSDNTSTLAMIDSVDAHGLQRMQTSKSETDFKFKGKDYHSLVSRTPDDNLPHVTNELGDTYVDNKIVLHLTRG
NETVLNKTFTKNDFSSVVDANFLSKSILEGIVYDKTTPQGIVYAASVCYPQTDLYMPLSITITADGKMSIQKVDILEEDY
DDEAPN
A,B
JCSG-416984
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
ATCC 8483
sample
411476
Bacteroides ovatus
562
Escherichia Coli
PB1
Plasmid
SpeedET
1
2.14
42.60
VAPOR DIFFUSION, SITTING DROP
2.0 M ammonium sulfate, 0.01 M TCEP Hydrochloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
Joint Center for Structural Genomics
JCSG
PSI:Biology
software
database_2
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Structure summary
Refinement description
Database references
Derived calculations
1
0
2013-02-13
1
1
2014-12-24
1
2
2017-11-15
1
3
2023-02-01
_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
Y
RCSB
Y
RCSB
2012-12-11
REL
REL
SO4
SULFATE ION
EDO
1,2-ETHANEDIOL
HOH
water
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 19-183 OF THE TARGET SEQUENCE.
SO4
200
2
SO4
SO4
201
A
EDO
202
3
EDO
EDO
202
A
EDO
201
3
EDO
EDO
201
B
HOH
203
4
HOH
HOH
301
A
HOH
206
4
HOH
HOH
302
A
HOH
207
4
HOH
HOH
303
A
HOH
209
4
HOH
HOH
304
A
HOH
210
4
HOH
HOH
305
A
HOH
211
4
HOH
HOH
306
A
HOH
212
4
HOH
HOH
307
A
HOH
213
4
HOH
HOH
308
A
HOH
215
4
HOH
HOH
309
A
HOH
218
4
HOH
HOH
310
A
HOH
220
4
HOH
HOH
311
A
HOH
222
4
HOH
HOH
312
A
HOH
223
4
HOH
HOH
313
A
HOH
224
4
HOH
HOH
314
A
HOH
235
4
HOH
HOH
315
A
HOH
237
4
HOH
HOH
316
A
HOH
239
4
HOH
HOH
317
A
HOH
240
4
HOH
HOH
318
A
HOH
243
4
HOH
HOH
319
A
HOH
246
4
HOH
HOH
320
A
HOH
251
4
HOH
HOH
321
A
HOH
252
4
HOH
HOH
322
A
HOH
253
4
HOH
HOH
323
A
HOH
254
4
HOH
HOH
324
A
HOH
257
4
HOH
HOH
325
A
HOH
260
4
HOH
HOH
326
A
HOH
265
4
HOH
HOH
327
A
HOH
266
4
HOH
HOH
328
A
HOH
268
4
HOH
HOH
329
A
HOH
270
4
HOH
HOH
330
A
HOH
273
4
HOH
HOH
331
A
HOH
274
4
HOH
HOH
332
A
HOH
275
4
HOH
HOH
333
A
HOH
276
4
HOH
HOH
334
A
HOH
277
4
HOH
HOH
335
A
HOH
279
4
HOH
HOH
336
A
HOH
280
4
HOH
HOH
337
A
HOH
284
4
HOH
HOH
338
A
HOH
287
4
HOH
HOH
339
A
HOH
288
4
HOH
HOH
340
A
HOH
290
4
HOH
HOH
341
A
HOH
291
4
HOH
HOH
342
A
HOH
294
4
HOH
HOH
343
A
HOH
298
4
HOH
HOH
344
A
HOH
299
4
HOH
HOH
345
A
HOH
302
4
HOH
HOH
346
A
HOH
303
4
HOH
HOH
347
A
HOH
304
4
HOH
HOH
348
A
HOH
305
4
HOH
HOH
349
A
HOH
310
4
HOH
HOH
350
A
HOH
311
4
HOH
HOH
351
A
HOH
204
4
HOH
HOH
301
B
HOH
205
4
HOH
HOH
302
B
HOH
208
4
HOH
HOH
303
B
HOH
214
4
HOH
HOH
304
B
HOH
216
4
HOH
HOH
305
B
HOH
217
4
HOH
HOH
306
B
HOH
219
4
HOH
HOH
307
B
HOH
221
4
HOH
HOH
308
B
HOH
225
4
HOH
HOH
309
B
HOH
226
4
HOH
HOH
310
B
HOH
227
4
HOH
HOH
311
B
HOH
228
4
HOH
HOH
312
B
HOH
229
4
HOH
HOH
313
B
HOH
230
4
HOH
HOH
314
B
HOH
231
4
HOH
HOH
315
B
HOH
232
4
HOH
HOH
316
B
HOH
233
4
HOH
HOH
317
B
HOH
234
4
HOH
HOH
318
B
HOH
236
4
HOH
HOH
319
B
HOH
238
4
HOH
HOH
320
B
HOH
241
4
HOH
HOH
321
B
HOH
242
4
HOH
HOH
322
B
HOH
244
4
HOH
HOH
323
B
HOH
245
4
HOH
HOH
324
B
HOH
247
4
HOH
HOH
325
B
HOH
248
4
HOH
HOH
326
B
HOH
249
4
HOH
HOH
327
B
HOH
250
4
HOH
HOH
328
B
HOH
255
4
HOH
HOH
329
B
HOH
256
4
HOH
HOH
330
B
HOH
258
4
HOH
HOH
331
B
HOH
259
4
HOH
HOH
332
B
HOH
261
4
HOH
HOH
333
B
HOH
262
4
HOH
HOH
334
B
HOH
263
4
HOH
HOH
335
B
HOH
264
4
HOH
HOH
336
B
HOH
267
4
HOH
HOH
337
B
HOH
269
4
HOH
HOH
338
B
HOH
271
4
HOH
HOH
339
B
HOH
272
4
HOH
HOH
340
B
HOH
278
4
HOH
HOH
341
B
HOH
281
4
HOH
HOH
342
B
HOH
282
4
HOH
HOH
343
B
HOH
283
4
HOH
HOH
344
B
HOH
285
4
HOH
HOH
345
B
HOH
286
4
HOH
HOH
346
B
HOH
289
4
HOH
HOH
347
B
HOH
292
4
HOH
HOH
348
B
HOH
293
4
HOH
HOH
349
B
HOH
295
4
HOH
HOH
350
B
HOH
296
4
HOH
HOH
351
B
HOH
297
4
HOH
HOH
352
B
HOH
300
4
HOH
HOH
353
B
HOH
301
4
HOH
HOH
354
B
HOH
306
4
HOH
HOH
355
B
HOH
307
4
HOH
HOH
356
B
HOH
308
4
HOH
HOH
357
B
HOH
309
4
HOH
HOH
358
B
n
1
18
A
n
2
19
A
n
3
20
A
n
4
21
A
n
5
22
A
n
6
23
A
n
7
24
A
n
8
25
A
n
9
26
A
n
10
27
A
n
11
28
A
n
12
29
A
n
13
30
A
n
14
31
A
n
15
32
A
n
16
33
A
n
17
34
A
n
18
35
A
n
19
36
A
n
20
37
A
n
21
38
A
n
22
39
A
n
23
40
A
n
24
41
A
GLY
42
n
25
GLY
42
A
LEU
43
n
26
LEU
43
A
GLN
44
n
27
GLN
44
A
ARG
45
n
28
ARG
45
A
MSE
46
n
29
MSE
46
A
GLN
47
n
30
GLN
47
A
THR
48
n
31
THR
48
A
SER
49
n
32
SER
49
A
LYS
50
n
33
LYS
50
A
SER
51
n
34
SER
51
A
GLU
52
n
35
GLU
52
A
THR
53
n
36
THR
53
A
ASP
54
n
37
ASP
54
A
PHE
55
n
38
PHE
55
A
LYS
56
n
39
LYS
56
A
PHE
57
n
40
PHE
57
A
LYS
58
n
41
LYS
58
A
GLY
59
n
42
GLY
59
A
LYS
60
n
43
LYS
60
A
ASP
61
n
44
ASP
61
A
TYR
62
n
45
TYR
62
A
HIS
63
n
46
HIS
63
A
SER
64
n
47
SER
64
A
LEU
65
n
48
LEU
65
A
VAL
66
n
49
VAL
66
A
SER
67
n
50
SER
67
A
ARG
68
n
51
ARG
68
A
THR
69
n
52
THR
69
A
PRO
70
n
53
PRO
70
A
ASP
71
n
54
ASP
71
A
ASP
72
n
55
ASP
72
A
ASN
73
n
56
ASN
73
A
LEU
74
n
57
LEU
74
A
PRO
75
n
58
PRO
75
A
HIS
76
n
59
HIS
76
A
VAL
77
n
60
VAL
77
A
THR
78
n
61
THR
78
A
ASN
79
n
62
ASN
79
A
GLU
80
n
63
GLU
80
A
LEU
81
n
64
LEU
81
A
GLY
82
n
65
GLY
82
A
ASP
83
n
66
ASP
83
A
THR
84
n
67
THR
84
A
TYR
85
n
68
TYR
85
A
VAL
86
n
69
VAL
86
A
ASP
87
n
70
ASP
87
A
ASN
88
n
71
ASN
88
A
LYS
89
n
72
LYS
89
A
ILE
90
n
73
ILE
90
A
VAL
91
n
74
VAL
91
A
LEU
92
n
75
LEU
92
A
HIS
93
n
76
HIS
93
A
LEU
94
n
77
LEU
94
A
THR
95
n
78
THR
95
A
ARG
96
n
79
ARG
96
A
GLY
97
n
80
GLY
97
A
ASN
98
n
81
ASN
98
A
GLU
99
n
82
GLU
99
A
THR
100
n
83
THR
100
A
VAL
101
n
84
VAL
101
A
LEU
102
n
85
LEU
102
A
ASN
103
n
86
ASN
103
A
LYS
104
n
87
LYS
104
A
THR
105
n
88
THR
105
A
PHE
106
n
89
PHE
106
A
THR
107
n
90
THR
107
A
LYS
108
n
91
LYS
108
A
ASN
109
n
92
ASN
109
A
ASP
110
n
93
ASP
110
A
PHE
111
n
94
PHE
111
A
SER
112
n
95
SER
112
A
SER
113
n
96
SER
113
A
VAL
114
n
97
VAL
114
A
VAL
115
n
98
VAL
115
A
ASP
116
n
99
ASP
116
A
ALA
117
n
100
ALA
117
A
ASN
118
n
101
ASN
118
A
PHE
119
n
102
PHE
119
A
LEU
120
n
103
LEU
120
A
SER
121
n
104
SER
121
A
LYS
122
n
105
LYS
122
A
SER
123
n
106
SER
123
A
ILE
124
n
107
ILE
124
A
LEU
125
n
108
LEU
125
A
GLU
126
n
109
GLU
126
A
GLY
127
n
110
GLY
127
A
ILE
128
n
111
ILE
128
A
VAL
129
n
112
VAL
129
A
TYR
130
n
113
TYR
130
A
ASP
131
n
114
ASP
131
A
LYS
132
n
115
LYS
132
A
THR
133
n
116
THR
133
A
THR
134
n
117
THR
134
A
PRO
135
n
118
PRO
135
A
GLN
136
n
119
GLN
136
A
GLY
137
n
120
GLY
137
A
ILE
138
n
121
ILE
138
A
VAL
139
n
122
VAL
139
A
TYR
140
n
123
TYR
140
A
ALA
141
n
124
ALA
141
A
ALA
142
n
125
ALA
142
A
SER
143
n
126
SER
143
A
VAL
144
n
127
VAL
144
A
CYS
145
n
128
CYS
145
A
TYR
146
n
129
TYR
146
A
PRO
147
n
130
PRO
147
A
GLN
148
n
131
GLN
148
A
THR
149
n
132
THR
149
A
ASP
150
n
133
ASP
150
A
LEU
151
n
134
LEU
151
A
TYR
152
n
135
TYR
152
A
MSE
153
n
136
MSE
153
A
PRO
154
n
137
PRO
154
A
LEU
155
n
138
LEU
155
A
SER
156
n
139
SER
156
A
ILE
157
n
140
ILE
157
A
THR
158
n
141
THR
158
A
ILE
159
n
142
ILE
159
A
THR
160
n
143
THR
160
A
ALA
161
n
144
ALA
161
A
ASP
162
n
145
ASP
162
A
GLY
163
n
146
GLY
163
A
LYS
164
n
147
LYS
164
A
MSE
165
n
148
MSE
165
A
SER
166
n
149
SER
166
A
ILE
167
n
150
ILE
167
A
GLN
168
n
151
GLN
168
A
LYS
169
n
152
LYS
169
A
VAL
170
n
153
VAL
170
A
ASP
171
n
154
ASP
171
A
ILE
172
n
155
ILE
172
A
LEU
173
n
156
LEU
173
A
GLU
174
n
157
GLU
174
A
GLU
175
n
158
GLU
175
A
ASP
176
n
159
ASP
176
A
TYR
177
n
160
TYR
177
A
n
161
178
A
n
162
179
A
n
163
180
A
n
164
181
A
n
165
182
A
n
166
183
A
n
1
18
B
n
2
19
B
n
3
20
B
n
4
21
B
n
5
22
B
n
6
23
B
n
7
24
B
n
8
25
B
n
9
26
B
n
10
27
B
n
11
28
B
n
12
29
B
n
13
30
B
n
14
31
B
n
15
32
B
n
16
33
B
n
17
34
B
n
18
35
B
n
19
36
B
n
20
37
B
n
21
38
B
n
22
39
B
n
23
40
B
n
24
41
B
GLY
42
n
25
GLY
42
B
LEU
43
n
26
LEU
43
B
GLN
44
n
27
GLN
44
B
ARG
45
n
28
ARG
45
B
MSE
46
n
29
MSE
46
B
GLN
47
n
30
GLN
47
B
THR
48
n
31
THR
48
B
SER
49
n
32
SER
49
B
LYS
50
n
33
LYS
50
B
SER
51
n
34
SER
51
B
GLU
52
n
35
GLU
52
B
THR
53
n
36
THR
53
B
ASP
54
n
37
ASP
54
B
PHE
55
n
38
PHE
55
B
LYS
56
n
39
LYS
56
B
PHE
57
n
40
PHE
57
B
LYS
58
n
41
LYS
58
B
GLY
59
n
42
GLY
59
B
LYS
60
n
43
LYS
60
B
ASP
61
n
44
ASP
61
B
TYR
62
n
45
TYR
62
B
HIS
63
n
46
HIS
63
B
SER
64
n
47
SER
64
B
LEU
65
n
48
LEU
65
B
VAL
66
n
49
VAL
66
B
SER
67
n
50
SER
67
B
ARG
68
n
51
ARG
68
B
THR
69
n
52
THR
69
B
PRO
70
n
53
PRO
70
B
ASP
71
n
54
ASP
71
B
ASP
72
n
55
ASP
72
B
ASN
73
n
56
ASN
73
B
LEU
74
n
57
LEU
74
B
PRO
75
n
58
PRO
75
B
HIS
76
n
59
HIS
76
B
VAL
77
n
60
VAL
77
B
THR
78
n
61
THR
78
B
ASN
79
n
62
ASN
79
B
GLU
80
n
63
GLU
80
B
LEU
81
n
64
LEU
81
B
GLY
82
n
65
GLY
82
B
ASP
83
n
66
ASP
83
B
THR
84
n
67
THR
84
B
TYR
85
n
68
TYR
85
B
VAL
86
n
69
VAL
86
B
ASP
87
n
70
ASP
87
B
ASN
88
n
71
ASN
88
B
LYS
89
n
72
LYS
89
B
ILE
90
n
73
ILE
90
B
VAL
91
n
74
VAL
91
B
LEU
92
n
75
LEU
92
B
HIS
93
n
76
HIS
93
B
LEU
94
n
77
LEU
94
B
THR
95
n
78
THR
95
B
ARG
96
n
79
ARG
96
B
GLY
97
n
80
GLY
97
B
ASN
98
n
81
ASN
98
B
GLU
99
n
82
GLU
99
B
THR
100
n
83
THR
100
B
VAL
101
n
84
VAL
101
B
LEU
102
n
85
LEU
102
B
ASN
103
n
86
ASN
103
B
LYS
104
n
87
LYS
104
B
THR
105
n
88
THR
105
B
PHE
106
n
89
PHE
106
B
THR
107
n
90
THR
107
B
LYS
108
n
91
LYS
108
B
ASN
109
n
92
ASN
109
B
ASP
110
n
93
ASP
110
B
PHE
111
n
94
PHE
111
B
SER
112
n
95
SER
112
B
SER
113
n
96
SER
113
B
VAL
114
n
97
VAL
114
B
VAL
115
n
98
VAL
115
B
ASP
116
n
99
ASP
116
B
ALA
117
n
100
ALA
117
B
ASN
118
n
101
ASN
118
B
PHE
119
n
102
PHE
119
B
LEU
120
n
103
LEU
120
B
SER
121
n
104
SER
121
B
LYS
122
n
105
LYS
122
B
SER
123
n
106
SER
123
B
ILE
124
n
107
ILE
124
B
LEU
125
n
108
LEU
125
B
GLU
126
n
109
GLU
126
B
GLY
127
n
110
GLY
127
B
ILE
128
n
111
ILE
128
B
VAL
129
n
112
VAL
129
B
TYR
130
n
113
TYR
130
B
ASP
131
n
114
ASP
131
B
LYS
132
n
115
LYS
132
B
THR
133
n
116
THR
133
B
THR
134
n
117
THR
134
B
PRO
135
n
118
PRO
135
B
GLN
136
n
119
GLN
136
B
GLY
137
n
120
GLY
137
B
ILE
138
n
121
ILE
138
B
VAL
139
n
122
VAL
139
B
TYR
140
n
123
TYR
140
B
ALA
141
n
124
ALA
141
B
ALA
142
n
125
ALA
142
B
SER
143
n
126
SER
143
B
VAL
144
n
127
VAL
144
B
CYS
145
n
128
CYS
145
B
TYR
146
n
129
TYR
146
B
PRO
147
n
130
PRO
147
B
GLN
148
n
131
GLN
148
B
THR
149
n
132
THR
149
B
ASP
150
n
133
ASP
150
B
LEU
151
n
134
LEU
151
B
TYR
152
n
135
TYR
152
B
MSE
153
n
136
MSE
153
B
PRO
154
n
137
PRO
154
B
LEU
155
n
138
LEU
155
B
SER
156
n
139
SER
156
B
ILE
157
n
140
ILE
157
B
THR
158
n
141
THR
158
B
ILE
159
n
142
ILE
159
B
THR
160
n
143
THR
160
B
ALA
161
n
144
ALA
161
B
ASP
162
n
145
ASP
162
B
GLY
163
n
146
GLY
163
B
LYS
164
n
147
LYS
164
B
MSE
165
n
148
MSE
165
B
SER
166
n
149
SER
166
B
ILE
167
n
150
ILE
167
B
GLN
168
n
151
GLN
168
B
LYS
169
n
152
LYS
169
B
VAL
170
n
153
VAL
170
B
ASP
171
n
154
ASP
171
B
ILE
172
n
155
ILE
172
B
LEU
173
n
156
LEU
173
B
GLU
174
n
157
GLU
174
B
GLU
175
n
158
GLU
175
B
ASP
176
n
159
ASP
176
B
TYR
177
n
160
TYR
177
B
n
161
178
B
n
162
179
B
n
163
180
B
n
164
181
B
n
165
182
B
n
166
183
B
2.2447
0.0122
0.2290
3.7067
-0.1810
2.6072
-0.0953
0.0608
-0.1334
-0.1562
0.0011
-0.1527
0.3490
0.1049
0.0942
-0.0756
0.0620
-0.1011
-0.2837
0.0203
-0.0011
refined
5.4498
3.2450
16.1178
X-RAY DIFFRACTION
2.6632
-1.0235
0.3712
5.1265
0.3007
3.1113
0.0257
0.0389
0.0235
-0.3387
-0.0752
0.0120
-0.2486
-0.1162
0.0496
-0.0759
0.0570
-0.1116
-0.2987
-0.0105
-0.0494
refined
-4.2189
20.7631
16.2740
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
{ A|42-177 }
X-RAY DIFFRACTION
2
{ B|42-177 }
author_and_software_defined_assembly
PISA
4
tetrameric
9040
-47
24710
A
MSE
46
SELENOMETHIONINE
A
MSE
29
MET
A
MSE
153
SELENOMETHIONINE
A
MSE
136
MET
A
MSE
165
SELENOMETHIONINE
A
MSE
148
MET
B
MSE
46
SELENOMETHIONINE
B
MSE
29
MET
B
MSE
153
SELENOMETHIONINE
B
MSE
136
MET
B
MSE
165
SELENOMETHIONINE
B
MSE
148
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_555
-x,y,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
A
N
GLN
44
A
N
GLN
27
A
O
THR
84
A
O
THR
67
A
O
TYR
85
A
O
TYR
68
A
N
VAL
77
A
N
VAL
60
A
O
PHE
106
A
O
PHE
89
A
N
ILE
90
A
N
ILE
73
A
O
HIS
93
A
O
HIS
76
A
N
LEU
65
A
N
LEU
48
A
O
TYR
62
A
O
TYR
45
A
N
PHE
55
A
N
PHE
38
A
N
ASP
54
A
N
ASP
37
B
O
GLU
52
B
O
GLU
35
B
N
PHE
55
B
N
PHE
38
B
O
TYR
62
B
O
TYR
45
B
N
LEU
65
B
N
LEU
48
B
O
HIS
93
B
O
HIS
76
B
N
ILE
90
B
N
ILE
73
B
O
PHE
106
B
O
PHE
89
A
N
VAL
129
A
N
VAL
112
A
O
ALA
141
A
O
ALA
124
A
N
ILE
138
A
N
ILE
121
A
O
ILE
159
A
O
ILE
142
A
N
THR
158
A
N
THR
141
A
O
SER
166
A
O
SER
149
B
N
VAL
77
B
N
VAL
60
B
O
TYR
85
B
O
TYR
68
B
N
LYS
132
B
N
LYS
115
B
O
VAL
139
B
O
VAL
122
B
N
ILE
138
B
N
ILE
121
B
O
ILE
159
B
O
ILE
142
B
N
THR
158
B
N
THR
141
B
O
SER
166
B
O
SER
149
1
A
CG
GLN
47
A
CG
GLN
30
1
Y
1
A
CD
GLN
47
A
CD
GLN
30
1
Y
1
A
OE1
GLN
47
A
OE1
GLN
30
1
Y
1
A
NE2
GLN
47
A
NE2
GLN
30
1
Y
1
A
CG
GLU
80
A
CG
GLU
63
1
Y
1
A
CD
GLU
80
A
CD
GLU
63
1
Y
1
A
OE1
GLU
80
A
OE1
GLU
63
1
Y
1
A
OE2
GLU
80
A
OE2
GLU
63
1
Y
1
A
CG
LEU
81
A
CG
LEU
64
1
Y
1
A
CD1
LEU
81
A
CD1
LEU
64
1
Y
1
A
CD2
LEU
81
A
CD2
LEU
64
1
Y
1
A
CG
ASN
118
A
CG
ASN
101
1
Y
1
A
OD1
ASN
118
A
OD1
ASN
101
1
Y
1
A
ND2
ASN
118
A
ND2
ASN
101
1
Y
1
A
CG
PHE
119
A
CG
PHE
102
1
Y
1
A
CD1
PHE
119
A
CD1
PHE
102
1
Y
1
A
CD2
PHE
119
A
CD2
PHE
102
1
Y
1
A
CE1
PHE
119
A
CE1
PHE
102
1
Y
1
A
CE2
PHE
119
A
CE2
PHE
102
1
Y
1
A
CZ
PHE
119
A
CZ
PHE
102
1
Y
1
A
CG
GLN
148
A
CG
GLN
131
1
Y
1
A
CD
GLN
148
A
CD
GLN
131
1
Y
1
A
OE1
GLN
148
A
OE1
GLN
131
1
Y
1
A
NE2
GLN
148
A
NE2
GLN
131
1
Y
1
A
CG
ASP
150
A
CG
ASP
133
1
Y
1
A
OD1
ASP
150
A
OD1
ASP
133
1
Y
1
A
OD2
ASP
150
A
OD2
ASP
133
1
Y
1
B
CG
GLU
80
B
CG
GLU
63
1
Y
1
B
CD
GLU
80
B
CD
GLU
63
1
Y
1
B
OE1
GLU
80
B
OE1
GLU
63
1
Y
1
B
OE2
GLU
80
B
OE2
GLU
63
1
Y
1
B
CG
LEU
81
B
CG
LEU
64
1
Y
1
B
CD1
LEU
81
B
CD1
LEU
64
1
Y
1
B
CD2
LEU
81
B
CD2
LEU
64
1
Y
1
B
CG
ASP
83
B
CG
ASP
66
1
Y
1
B
OD1
ASP
83
B
OD1
ASP
66
1
Y
1
B
OD2
ASP
83
B
OD2
ASP
66
1
Y
1
B
CG
ASN
118
B
CG
ASN
101
1
Y
1
B
OD1
ASN
118
B
OD1
ASN
101
1
Y
1
B
ND2
ASN
118
B
ND2
ASN
101
1
Y
1
B
CG
GLN
148
B
CG
GLN
131
1
Y
1
B
CD
GLN
148
B
CD
GLN
131
1
Y
1
B
OE1
GLN
148
B
OE1
GLN
131
1
Y
1
B
NE2
GLN
148
B
NE2
GLN
131
1
Y
1
B
CG
ASP
176
B
CG
ASP
159
1
Y
1
B
OD1
ASP
176
B
OD1
ASP
159
1
Y
1
B
OD2
ASP
176
B
OD2
ASP
159
1
Y
1
B
CG
TYR
177
B
CG
TYR
160
1
Y
1
B
CD1
TYR
177
B
CD1
TYR
160
1
Y
1
B
CD2
TYR
177
B
CD2
TYR
160
1
Y
1
B
CE1
TYR
177
B
CE1
TYR
160
1
Y
1
B
CE2
TYR
177
B
CE2
TYR
160
1
Y
1
B
CZ
TYR
177
B
CZ
TYR
160
1
Y
1
B
OH
TYR
177
B
OH
TYR
160
1
Y
1
A
GLY
18
A
GLY
1
1
Y
1
A
CYS
19
A
CYS
2
1
Y
1
A
GLY
20
A
GLY
3
1
Y
1
A
GLY
21
A
GLY
4
1
Y
1
A
LYS
22
A
LYS
5
1
Y
1
A
LYS
23
A
LYS
6
1
Y
1
A
GLY
24
A
GLY
7
1
Y
1
A
SER
25
A
SER
8
1
Y
1
A
SER
26
A
SER
9
1
Y
1
A
ASP
27
A
ASP
10
1
Y
1
A
ASN
28
A
ASN
11
1
Y
1
A
THR
29
A
THR
12
1
Y
1
A
SER
30
A
SER
13
1
Y
1
A
THR
31
A
THR
14
1
Y
1
A
LEU
32
A
LEU
15
1
Y
1
A
ALA
33
A
ALA
16
1
Y
1
A
MSE
34
A
MSE
17
1
Y
1
A
ILE
35
A
ILE
18
1
Y
1
A
ASP
36
A
ASP
19
1
Y
1
A
SER
37
A
SER
20
1
Y
1
A
VAL
38
A
VAL
21
1
Y
1
A
ASP
39
A
ASP
22
1
Y
1
A
ALA
40
A
ALA
23
1
Y
1
A
HIS
41
A
HIS
24
1
Y
1
A
ASP
178
A
ASP
161
1
Y
1
A
ASP
179
A
ASP
162
1
Y
1
A
GLU
180
A
GLU
163
1
Y
1
A
ALA
181
A
ALA
164
1
Y
1
A
PRO
182
A
PRO
165
1
Y
1
A
ASN
183
A
ASN
166
1
Y
1
B
GLY
18
B
GLY
1
1
Y
1
B
CYS
19
B
CYS
2
1
Y
1
B
GLY
20
B
GLY
3
1
Y
1
B
GLY
21
B
GLY
4
1
Y
1
B
LYS
22
B
LYS
5
1
Y
1
B
LYS
23
B
LYS
6
1
Y
1
B
GLY
24
B
GLY
7
1
Y
1
B
SER
25
B
SER
8
1
Y
1
B
SER
26
B
SER
9
1
Y
1
B
ASP
27
B
ASP
10
1
Y
1
B
ASN
28
B
ASN
11
1
Y
1
B
THR
29
B
THR
12
1
Y
1
B
SER
30
B
SER
13
1
Y
1
B
THR
31
B
THR
14
1
Y
1
B
LEU
32
B
LEU
15
1
Y
1
B
ALA
33
B
ALA
16
1
Y
1
B
MSE
34
B
MSE
17
1
Y
1
B
ILE
35
B
ILE
18
1
Y
1
B
ASP
36
B
ASP
19
1
Y
1
B
SER
37
B
SER
20
1
Y
1
B
VAL
38
B
VAL
21
1
Y
1
B
ASP
39
B
ASP
22
1
Y
1
B
ALA
40
B
ALA
23
1
Y
1
B
HIS
41
B
HIS
24
1
Y
1
B
ASP
178
B
ASP
161
1
Y
1
B
ASP
179
B
ASP
162
1
Y
1
B
GLU
180
B
GLU
163
1
Y
1
B
ALA
181
B
ALA
164
1
Y
1
B
PRO
182
B
PRO
165
1
Y
1
B
ASN
183
B
ASN
166
1
Y
1
A
ASP
131
-109.83
-64.33
155.640
61.5614
29.510
-4.0304
0.0000
0.3249
11.0061
0.0000
-6.9757
0.9387
0.9162
1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. 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. 5. NCS RESTRAINTS WERE APPLIED DURING REFINEMENT USING LSSR (-AUTONCS) IN BUSTER. 6. MAD PHASE RESTRAINTS WERE USED DURING REFINEMENT. 7. SULPFATE (SO4) IONS AND EDO (ETHYLENE GLYCOL) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED.
0.2332
0.2070
0.2086
2.1500
24.947
933
16913
5.5200
99.2900
1.000
0.500
RANDOM
1
THROUGHOUT
0.000
MAD
0.412
2.1500
24.947
109
2216
13
0
2094
1190
SINUSOIDAL
2.000
52
HARMONIC
2.000
610
HARMONIC
5.000
4202
HARMONIC
20.000
303
SEMIHARMONIC
5.000
4310
SEMIHARMONIC
4.000
0.007
4202
HARMONIC
2.000
1.000
7597
HARMONIC
2.000
3.110
2.700
0.2519
0.2277
0.2290
2.2800
133
2534
2667
9
4.9900
99.2900
44.273
2.15
24.947
4ID2
16940
-3.000
0.048
1
10.010
96.500
0.766
2.150
2.230
1.2
5725
3127
1
89.400
0.587
2.230
2.320
1.6
6074
3250
1
97.300
0.449
2.320
2.420
2.0
5870
3136
1
97.200
0.396
2.420
2.550
2.4
6184
3329
1
97.700
0.239
2.550
2.710
3.6
6118
3276
1
97.600
0.154
2.710
2.920
5.4
6279
3344
1
98.200
0.076
2.920
3.210
9.9
6059
3232
1
97.700
0.039
3.210
3.670
17.3
6084
3260
1
97.100
0.027
3.670
4.610
24.9
6005
3234
1
96.500
0.018
4.610
31.2
6203
3324
1
96.800
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
Wolfgang Kabsch
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html
XSCALE
package
March 15, 2012
refinement
Gerard Bricogne
buster-develop@GlobalPhasing.com
http://www.globalphasing.com/buster/
BUSTER-TNT
program
2.10.0
data reduction
XDS
phasing
SHELXD
refinement
BUSTER
2.10.0
Y
Crystal structure of a DUF4738 family protein (BACOVA_05496) from Bacteroides ovatus ATCC 8483 at 2.15 A resolution
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
4
N
N
4
N
N
A
THR
107
A
THR
90
HELX_P
A
SER
112
A
SER
95
5
1
6
A
ASP
116
A
ASP
99
HELX_P
A
LYS
122
A
LYS
105
1
2
7
B
THR
107
B
THR
90
HELX_P
B
SER
112
B
SER
95
5
3
6
B
ASP
116
B
ASP
99
HELX_P
B
LYS
122
B
LYS
105
1
4
7
covale
1.336
both
A
ARG
45
A
C
ARG
28
1_555
A
MSE
46
A
N
MSE
29
1_555
covale
1.336
both
A
MSE
46
A
C
MSE
29
1_555
A
GLN
47
A
N
GLN
30
1_555
covale
1.335
both
A
TYR
152
A
C
TYR
135
1_555
A
MSE
153
A
N
MSE
136
1_555
covale
1.345
both
A
MSE
153
A
C
MSE
136
1_555
A
PRO
154
A
N
PRO
137
1_555
covale
1.334
both
A
LYS
164
A
C
LYS
147
1_555
A
MSE
165
A
N
MSE
148
1_555
covale
1.348
both
A
MSE
165
A
C
MSE
148
1_555
A
SER
166
A
N
SER
149
1_555
covale
1.363
both
B
ARG
45
B
C
ARG
28
1_555
B
MSE
46
B
N
MSE
29
1_555
covale
1.334
both
B
MSE
46
B
C
MSE
29
1_555
B
GLN
47
B
N
GLN
30
1_555
covale
1.321
both
B
TYR
152
B
C
TYR
135
1_555
B
MSE
153
B
N
MSE
136
1_555
covale
1.348
both
B
MSE
153
B
C
MSE
136
1_555
B
PRO
154
B
N
PRO
137
1_555
covale
1.333
both
B
LYS
164
B
C
LYS
147
1_555
B
MSE
165
B
N
MSE
148
1_555
covale
1.346
both
B
MSE
165
B
C
MSE
148
1_555
B
SER
166
B
N
SER
149
1_555
STRUCTURAL GENOMICS, UNKNOWN FUNCTION
beta barrel like fold, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, UNKNOWN FUNCTION
A7M5V0_BACOV
UNP
1
19
A7M5V0
CGGKKGSSDNTSTLAMIDSVDAHGLQRMQTSKSETDFKFKGKDYHSLVSRTPDDNLPHVTNELGDTYVDNKIVLHLTRGN
ETVLNKTFTKNDFSSVVDANFLSKSILEGIVYDKTTPQGIVYAASVCYPQTDLYMPLSITITADGKMSIQKVDILEEDYD
DEAPN
19
183
4ID2
19
183
A7M5V0
A
1
2
166
19
183
4ID2
19
183
A7M5V0
B
1
2
166
1
expression tag
GLY
18
4ID2
A
A7M5V0
UNP
1
2
expression tag
GLY
18
4ID2
B
A7M5V0
UNP
1
3
8
4
2
4
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LEU
43
A
LEU
26
A
GLN
44
A
GLN
27
A
THR
84
A
THR
67
A
TYR
85
A
TYR
68
A
VAL
77
A
VAL
60
A
THR
78
A
THR
61
A
GLU
99
A
GLU
82
A
PHE
106
A
PHE
89
A
ASN
88
A
ASN
71
A
ARG
96
A
ARG
79
A
LYS
60
A
LYS
43
A
PRO
70
A
PRO
53
A
LYS
50
A
LYS
33
A
PHE
57
A
PHE
40
B
LYS
50
B
LYS
33
B
PHE
57
B
PHE
40
B
LYS
60
B
LYS
43
B
PRO
70
B
PRO
53
B
ASN
88
B
ASN
71
B
ARG
96
B
ARG
79
B
GLU
99
B
GLU
82
B
PHE
106
B
PHE
89
A
ILE
124
A
ILE
107
A
THR
133
A
THR
116
A
ILE
138
A
ILE
121
A
CYS
145
A
CYS
128
A
TYR
152
A
TYR
135
A
ILE
159
A
ILE
142
A
MSE
165
A
MSE
148
A
LYS
169
A
LYS
152
B
VAL
77
B
VAL
60
B
THR
78
B
THR
61
B
THR
84
B
THR
67
B
TYR
85
B
TYR
68
B
ILE
124
B
ILE
107
B
THR
133
B
THR
116
B
ILE
138
B
ILE
121
B
CYS
145
B
CYS
128
B
TYR
152
B
TYR
135
B
ILE
159
B
ILE
142
B
MSE
165
B
MSE
148
B
LYS
169
B
LYS
152
BINDING SITE FOR RESIDUE SO4 A 201
A
SO4
201
Software
7
BINDING SITE FOR RESIDUE EDO A 202
A
EDO
202
Software
3
BINDING SITE FOR RESIDUE EDO B 201
B
EDO
201
Software
6
A
ASP
71
A
ASP
54
7
1_555
A
ASN
73
A
ASN
56
7
1_555
A
HOH
301
F
HOH
7
1_555
A
HOH
314
F
HOH
7
1_555
B
ASP
71
B
ASP
54
7
3_545
B
ASN
73
B
ASN
56
7
3_545
B
LYS
89
B
LYS
72
7
3_545
A
CYS
145
A
CYS
128
3
1_555
A
PRO
147
A
PRO
130
3
1_555
A
HOH
343
F
HOH
3
1_555
A
THR
100
A
THR
83
6
4_556
A
ASN
103
A
ASN
86
6
4_556
B
THR
100
B
THR
83
6
1_555
B
ASN
103
B
ASN
86
6
1_555
B
HOH
328
G
HOH
6
1_555
B
HOH
330
G
HOH
6
1_555
5
C 1 2 1