0.022441
0.000000
0.001690
0.000000
0.018123
0.000000
0.000000
0.000000
0.021284
0.000000
0.000000
0.000000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
94.310
90.000
44.562
55.179
47.116
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 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 Domain of Unknown Function with an Immunoglobulin-like Beta-sandwich Fold (YP_001297618.1) from Bacteroides vulgatus ATCC 8482 at 1.70 A resolution
10.2210/pdb3d33/pdb
pdb_00003d33
100
1
Flat mirror (vertical focusing)
CCD
2008-04-11
MARMOSAIC 325 mm CCD
Single crystal Si(111) bent monochromator (horizontal focusing)
SINGLE WAVELENGTH
M
x-ray
1
1.0
BL11-1
SSRL
SYNCHROTRON
SSRL BEAMLINE BL11-1
11948.939
Domain of Unknown Function with an Immunoglobulin-like Beta-sandwich Fold
2
man
polymer
18.015
water
283
nat
water
no
yes
GANTTETPVKDVELDGRWDDPIRSAATNCPITVFTDGYLLTLKNASPDRD(MSE)TIRITD(MSE)AKGGVVYENDIPEV
QSAYITISIANFPAEEYKLEITGTPSGHLTGYFTKE
GANTTETPVKDVELDGRWDDPIRSAATNCPITVFTDGYLLTLKNASPDRDMTIRITDMAKGGVVYENDIPEVQSAYITIS
IANFPAEEYKLEITGTPSGHLTGYFTKE
A,B
390198
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
sample
YP_001297618.1, BVU_0276
435590
Bacteroides vulgatus ATCC 8482
Escherichia Coli
HK100
Plasmid
SpeedET
1
2.42
49.11
VAPOR DIFFUSION, SITTING DROP
5.9
0.2000M MgFormate, 20.0000% PEG-3350, No Buffer pH 5.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
277
Joint Center for Structural Genomics
JCSG
PSI, Protein Structure Initiative
pdbx_struct_assembly_auth_evidence
software
software
struct_conn
database_2
struct_ref_seq_dif
repository
Initial release
Advisory
Version format compliance
Author supporting evidence
Refinement description
Data collection
Derived calculations
Refinement description
Database references
1
0
2008-05-27
1
1
2011-07-13
1
2
2017-10-25
1
3
2019-07-24
1
4
2023-02-01
_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
Y
RCSB
Y
RCSB
2008-05-09
REL
REL
HOH
water
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. THE CLONED CONSTRUCT CONTAINS RESIDUES 28-134 OF THE FULL LENGTH PROTEIN. THIS REMOVED THE PUTATIVE SIGNAL PEPTIDE WHOSE PREDICTED CLEAVAGE SITE IS BETWEEN RESIDUES 28-29.
HOH
1
2
HOH
HOH
135
A
HOH
3
2
HOH
HOH
136
A
HOH
5
2
HOH
HOH
137
A
HOH
13
2
HOH
HOH
138
A
HOH
17
2
HOH
HOH
139
A
HOH
18
2
HOH
HOH
140
A
HOH
21
2
HOH
HOH
141
A
HOH
23
2
HOH
HOH
142
A
HOH
24
2
HOH
HOH
143
A
HOH
25
2
HOH
HOH
144
A
HOH
26
2
HOH
HOH
145
A
HOH
28
2
HOH
HOH
146
A
HOH
30
2
HOH
HOH
147
A
HOH
32
2
HOH
HOH
148
A
HOH
33
2
HOH
HOH
149
A
HOH
35
2
HOH
HOH
150
A
HOH
36
2
HOH
HOH
151
A
HOH
41
2
HOH
HOH
152
A
HOH
46
2
HOH
HOH
153
A
HOH
47
2
HOH
HOH
154
A
HOH
48
2
HOH
HOH
155
A
HOH
49
2
HOH
HOH
156
A
HOH
53
2
HOH
HOH
157
A
HOH
54
2
HOH
HOH
158
A
HOH
55
2
HOH
HOH
159
A
HOH
56
2
HOH
HOH
160
A
HOH
60
2
HOH
HOH
161
A
HOH
61
2
HOH
HOH
162
A
HOH
62
2
HOH
HOH
163
A
HOH
63
2
HOH
HOH
164
A
HOH
64
2
HOH
HOH
165
A
HOH
65
2
HOH
HOH
166
A
HOH
66
2
HOH
HOH
167
A
HOH
67
2
HOH
HOH
168
A
HOH
68
2
HOH
HOH
169
A
HOH
69
2
HOH
HOH
170
A
HOH
75
2
HOH
HOH
171
A
HOH
76
2
HOH
HOH
172
A
HOH
82
2
HOH
HOH
173
A
HOH
84
2
HOH
HOH
174
A
HOH
88
2
HOH
HOH
175
A
HOH
89
2
HOH
HOH
176
A
HOH
90
2
HOH
HOH
177
A
HOH
93
2
HOH
HOH
178
A
HOH
95
2
HOH
HOH
179
A
HOH
97
2
HOH
HOH
180
A
HOH
101
2
HOH
HOH
181
A
HOH
102
2
HOH
HOH
182
A
HOH
103
2
HOH
HOH
183
A
HOH
104
2
HOH
HOH
184
A
HOH
106
2
HOH
HOH
185
A
HOH
109
2
HOH
HOH
186
A
HOH
110
2
HOH
HOH
187
A
HOH
111
2
HOH
HOH
188
A
HOH
116
2
HOH
HOH
189
A
HOH
117
2
HOH
HOH
190
A
HOH
118
2
HOH
HOH
191
A
HOH
119
2
HOH
HOH
192
A
HOH
121
2
HOH
HOH
193
A
HOH
122
2
HOH
HOH
194
A
HOH
124
2
HOH
HOH
195
A
HOH
126
2
HOH
HOH
196
A
HOH
127
2
HOH
HOH
197
A
HOH
128
2
HOH
HOH
198
A
HOH
129
2
HOH
HOH
199
A
HOH
132
2
HOH
HOH
200
A
HOH
133
2
HOH
HOH
201
A
HOH
135
2
HOH
HOH
202
A
HOH
136
2
HOH
HOH
203
A
HOH
146
2
HOH
HOH
204
A
HOH
150
2
HOH
HOH
205
A
HOH
151
2
HOH
HOH
206
A
HOH
153
2
HOH
HOH
207
A
HOH
155
2
HOH
HOH
208
A
HOH
158
2
HOH
HOH
209
A
HOH
159
2
HOH
HOH
210
A
HOH
163
2
HOH
HOH
211
A
HOH
164
2
HOH
HOH
212
A
HOH
166
2
HOH
HOH
213
A
HOH
167
2
HOH
HOH
214
A
HOH
170
2
HOH
HOH
215
A
HOH
172
2
HOH
HOH
216
A
HOH
176
2
HOH
HOH
217
A
HOH
179
2
HOH
HOH
218
A
HOH
181
2
HOH
HOH
219
A
HOH
183
2
HOH
HOH
220
A
HOH
187
2
HOH
HOH
221
A
HOH
188
2
HOH
HOH
222
A
HOH
190
2
HOH
HOH
223
A
HOH
191
2
HOH
HOH
224
A
HOH
194
2
HOH
HOH
225
A
HOH
196
2
HOH
HOH
226
A
HOH
198
2
HOH
HOH
227
A
HOH
204
2
HOH
HOH
228
A
HOH
205
2
HOH
HOH
229
A
HOH
209
2
HOH
HOH
230
A
HOH
212
2
HOH
HOH
231
A
HOH
215
2
HOH
HOH
232
A
HOH
216
2
HOH
HOH
233
A
HOH
224
2
HOH
HOH
234
A
HOH
225
2
HOH
HOH
235
A
HOH
226
2
HOH
HOH
236
A
HOH
227
2
HOH
HOH
237
A
HOH
228
2
HOH
HOH
238
A
HOH
229
2
HOH
HOH
239
A
HOH
230
2
HOH
HOH
240
A
HOH
231
2
HOH
HOH
241
A
HOH
237
2
HOH
HOH
242
A
HOH
238
2
HOH
HOH
243
A
HOH
240
2
HOH
HOH
244
A
HOH
241
2
HOH
HOH
245
A
HOH
242
2
HOH
HOH
246
A
HOH
244
2
HOH
HOH
247
A
HOH
246
2
HOH
HOH
248
A
HOH
247
2
HOH
HOH
249
A
HOH
248
2
HOH
HOH
250
A
HOH
255
2
HOH
HOH
251
A
HOH
261
2
HOH
HOH
252
A
HOH
262
2
HOH
HOH
253
A
HOH
264
2
HOH
HOH
254
A
HOH
265
2
HOH
HOH
255
A
HOH
267
2
HOH
HOH
256
A
HOH
269
2
HOH
HOH
257
A
HOH
270
2
HOH
HOH
258
A
HOH
272
2
HOH
HOH
259
A
HOH
273
2
HOH
HOH
260
A
HOH
274
2
HOH
HOH
261
A
HOH
276
2
HOH
HOH
262
A
HOH
280
2
HOH
HOH
263
A
HOH
281
2
HOH
HOH
264
A
HOH
2
2
HOH
HOH
135
B
HOH
4
2
HOH
HOH
136
B
HOH
6
2
HOH
HOH
137
B
HOH
7
2
HOH
HOH
138
B
HOH
8
2
HOH
HOH
139
B
HOH
9
2
HOH
HOH
140
B
HOH
10
2
HOH
HOH
141
B
HOH
11
2
HOH
HOH
142
B
HOH
12
2
HOH
HOH
143
B
HOH
14
2
HOH
HOH
144
B
HOH
15
2
HOH
HOH
145
B
HOH
16
2
HOH
HOH
146
B
HOH
19
2
HOH
HOH
147
B
HOH
20
2
HOH
HOH
148
B
HOH
22
2
HOH
HOH
149
B
HOH
27
2
HOH
HOH
150
B
HOH
29
2
HOH
HOH
151
B
HOH
31
2
HOH
HOH
152
B
HOH
34
2
HOH
HOH
153
B
HOH
37
2
HOH
HOH
154
B
HOH
38
2
HOH
HOH
155
B
HOH
39
2
HOH
HOH
156
B
HOH
40
2
HOH
HOH
157
B
HOH
42
2
HOH
HOH
158
B
HOH
43
2
HOH
HOH
159
B
HOH
44
2
HOH
HOH
160
B
HOH
45
2
HOH
HOH
161
B
HOH
50
2
HOH
HOH
162
B
HOH
51
2
HOH
HOH
163
B
HOH
52
2
HOH
HOH
164
B
HOH
57
2
HOH
HOH
165
B
HOH
58
2
HOH
HOH
166
B
HOH
59
2
HOH
HOH
167
B
HOH
70
2
HOH
HOH
168
B
HOH
71
2
HOH
HOH
169
B
HOH
72
2
HOH
HOH
170
B
HOH
73
2
HOH
HOH
171
B
HOH
74
2
HOH
HOH
172
B
HOH
77
2
HOH
HOH
173
B
HOH
78
2
HOH
HOH
174
B
HOH
79
2
HOH
HOH
175
B
HOH
80
2
HOH
HOH
176
B
HOH
81
2
HOH
HOH
177
B
HOH
83
2
HOH
HOH
178
B
HOH
85
2
HOH
HOH
179
B
HOH
86
2
HOH
HOH
180
B
HOH
87
2
HOH
HOH
181
B
HOH
91
2
HOH
HOH
182
B
HOH
92
2
HOH
HOH
183
B
HOH
94
2
HOH
HOH
184
B
HOH
96
2
HOH
HOH
185
B
HOH
98
2
HOH
HOH
186
B
HOH
99
2
HOH
HOH
187
B
HOH
100
2
HOH
HOH
188
B
HOH
105
2
HOH
HOH
189
B
HOH
107
2
HOH
HOH
190
B
HOH
108
2
HOH
HOH
191
B
HOH
112
2
HOH
HOH
192
B
HOH
113
2
HOH
HOH
193
B
HOH
114
2
HOH
HOH
194
B
HOH
115
2
HOH
HOH
195
B
HOH
120
2
HOH
HOH
196
B
HOH
123
2
HOH
HOH
197
B
HOH
125
2
HOH
HOH
198
B
HOH
130
2
HOH
HOH
199
B
HOH
131
2
HOH
HOH
200
B
HOH
134
2
HOH
HOH
201
B
HOH
137
2
HOH
HOH
202
B
HOH
138
2
HOH
HOH
203
B
HOH
139
2
HOH
HOH
204
B
HOH
140
2
HOH
HOH
205
B
HOH
141
2
HOH
HOH
206
B
HOH
142
2
HOH
HOH
207
B
HOH
143
2
HOH
HOH
208
B
HOH
144
2
HOH
HOH
209
B
HOH
145
2
HOH
HOH
210
B
HOH
147
2
HOH
HOH
211
B
HOH
148
2
HOH
HOH
212
B
HOH
149
2
HOH
HOH
213
B
HOH
152
2
HOH
HOH
214
B
HOH
154
2
HOH
HOH
215
B
HOH
156
2
HOH
HOH
216
B
HOH
157
2
HOH
HOH
217
B
HOH
160
2
HOH
HOH
218
B
HOH
161
2
HOH
HOH
219
B
HOH
162
2
HOH
HOH
220
B
HOH
165
2
HOH
HOH
221
B
HOH
168
2
HOH
HOH
222
B
HOH
169
2
HOH
HOH
223
B
HOH
171
2
HOH
HOH
224
B
HOH
173
2
HOH
HOH
225
B
HOH
174
2
HOH
HOH
226
B
HOH
175
2
HOH
HOH
227
B
HOH
177
2
HOH
HOH
228
B
HOH
178
2
HOH
HOH
229
B
HOH
180
2
HOH
HOH
230
B
HOH
182
2
HOH
HOH
231
B
HOH
184
2
HOH
HOH
232
B
HOH
185
2
HOH
HOH
233
B
HOH
186
2
HOH
HOH
234
B
HOH
189
2
HOH
HOH
235
B
HOH
192
2
HOH
HOH
236
B
HOH
193
2
HOH
HOH
237
B
HOH
195
2
HOH
HOH
238
B
HOH
197
2
HOH
HOH
239
B
HOH
199
2
HOH
HOH
240
B
HOH
200
2
HOH
HOH
241
B
HOH
201
2
HOH
HOH
242
B
HOH
202
2
HOH
HOH
243
B
HOH
203
2
HOH
HOH
244
B
HOH
206
2
HOH
HOH
245
B
HOH
207
2
HOH
HOH
246
B
HOH
208
2
HOH
HOH
247
B
HOH
210
2
HOH
HOH
248
B
HOH
211
2
HOH
HOH
249
B
HOH
213
2
HOH
HOH
250
B
HOH
214
2
HOH
HOH
251
B
HOH
217
2
HOH
HOH
252
B
HOH
218
2
HOH
HOH
253
B
HOH
219
2
HOH
HOH
254
B
HOH
220
2
HOH
HOH
255
B
HOH
221
2
HOH
HOH
256
B
HOH
222
2
HOH
HOH
257
B
HOH
223
2
HOH
HOH
258
B
HOH
232
2
HOH
HOH
259
B
HOH
233
2
HOH
HOH
260
B
HOH
234
2
HOH
HOH
261
B
HOH
235
2
HOH
HOH
262
B
HOH
236
2
HOH
HOH
263
B
HOH
239
2
HOH
HOH
264
B
HOH
243
2
HOH
HOH
265
B
HOH
245
2
HOH
HOH
266
B
HOH
249
2
HOH
HOH
267
B
HOH
250
2
HOH
HOH
268
B
HOH
251
2
HOH
HOH
269
B
HOH
252
2
HOH
HOH
270
B
HOH
253
2
HOH
HOH
271
B
HOH
254
2
HOH
HOH
272
B
HOH
256
2
HOH
HOH
273
B
HOH
257
2
HOH
HOH
274
B
HOH
258
2
HOH
HOH
275
B
HOH
259
2
HOH
HOH
276
B
HOH
260
2
HOH
HOH
277
B
HOH
263
2
HOH
HOH
278
B
HOH
266
2
HOH
HOH
279
B
HOH
268
2
HOH
HOH
280
B
HOH
271
2
HOH
HOH
281
B
HOH
275
2
HOH
HOH
282
B
HOH
277
2
HOH
HOH
283
B
HOH
278
2
HOH
HOH
284
B
HOH
279
2
HOH
HOH
285
B
HOH
282
2
HOH
HOH
286
B
HOH
283
2
HOH
HOH
287
B
n
1
27
A
n
2
28
A
n
3
29
A
n
4
30
A
n
5
31
A
n
6
32
A
n
7
33
A
PRO
34
n
8
PRO
34
A
VAL
35
n
9
VAL
35
A
LYS
36
n
10
LYS
36
A
ASP
37
n
11
ASP
37
A
VAL
38
n
12
VAL
38
A
GLU
39
n
13
GLU
39
A
LEU
40
n
14
LEU
40
A
ASP
41
n
15
ASP
41
A
GLY
42
n
16
GLY
42
A
ARG
43
n
17
ARG
43
A
TRP
44
n
18
TRP
44
A
ASP
45
n
19
ASP
45
A
ASP
46
n
20
ASP
46
A
n
21
47
A
n
22
48
A
n
23
49
A
n
24
50
A
n
25
51
A
n
26
52
A
n
27
53
A
ASN
54
n
28
ASN
54
A
CYS
55
n
29
CYS
55
A
PRO
56
n
30
PRO
56
A
ILE
57
n
31
ILE
57
A
THR
58
n
32
THR
58
A
VAL
59
n
33
VAL
59
A
PHE
60
n
34
PHE
60
A
THR
61
n
35
THR
61
A
ASP
62
n
36
ASP
62
A
GLY
63
n
37
GLY
63
A
TYR
64
n
38
TYR
64
A
LEU
65
n
39
LEU
65
A
LEU
66
n
40
LEU
66
A
THR
67
n
41
THR
67
A
LEU
68
n
42
LEU
68
A
LYS
69
n
43
LYS
69
A
ASN
70
n
44
ASN
70
A
ALA
71
n
45
ALA
71
A
SER
72
n
46
SER
72
A
PRO
73
n
47
PRO
73
A
ASP
74
n
48
ASP
74
A
ARG
75
n
49
ARG
75
A
ASP
76
n
50
ASP
76
A
MSE
77
n
51
MSE
77
A
THR
78
n
52
THR
78
A
ILE
79
n
53
ILE
79
A
ARG
80
n
54
ARG
80
A
ILE
81
n
55
ILE
81
A
THR
82
n
56
THR
82
A
ASP
83
n
57
ASP
83
A
MSE
84
n
58
MSE
84
A
ALA
85
n
59
ALA
85
A
LYS
86
n
60
LYS
86
A
GLY
87
n
61
GLY
87
A
GLY
88
n
62
GLY
88
A
VAL
89
n
63
VAL
89
A
VAL
90
n
64
VAL
90
A
TYR
91
n
65
TYR
91
A
GLU
92
n
66
GLU
92
A
ASN
93
n
67
ASN
93
A
ASP
94
n
68
ASP
94
A
ILE
95
n
69
ILE
95
A
PRO
96
n
70
PRO
96
A
GLU
97
n
71
GLU
97
A
VAL
98
n
72
VAL
98
A
GLN
99
n
73
GLN
99
A
SER
100
n
74
SER
100
A
ALA
101
n
75
ALA
101
A
TYR
102
n
76
TYR
102
A
ILE
103
n
77
ILE
103
A
THR
104
n
78
THR
104
A
ILE
105
n
79
ILE
105
A
SER
106
n
80
SER
106
A
ILE
107
n
81
ILE
107
A
ALA
108
n
82
ALA
108
A
ASN
109
n
83
ASN
109
A
PHE
110
n
84
PHE
110
A
PRO
111
n
85
PRO
111
A
ALA
112
n
86
ALA
112
A
GLU
113
n
87
GLU
113
A
GLU
114
n
88
GLU
114
A
TYR
115
n
89
TYR
115
A
LYS
116
n
90
LYS
116
A
LEU
117
n
91
LEU
117
A
GLU
118
n
92
GLU
118
A
ILE
119
n
93
ILE
119
A
THR
120
n
94
THR
120
A
GLY
121
n
95
GLY
121
A
THR
122
n
96
THR
122
A
PRO
123
n
97
PRO
123
A
SER
124
n
98
SER
124
A
GLY
125
n
99
GLY
125
A
HIS
126
n
100
HIS
126
A
LEU
127
n
101
LEU
127
A
THR
128
n
102
THR
128
A
GLY
129
n
103
GLY
129
A
TYR
130
n
104
TYR
130
A
PHE
131
n
105
PHE
131
A
THR
132
n
106
THR
132
A
LYS
133
n
107
LYS
133
A
GLU
134
n
108
GLU
134
A
n
1
27
B
n
2
28
B
n
3
29
B
n
4
30
B
n
5
31
B
n
6
32
B
n
7
33
B
PRO
34
n
8
PRO
34
B
VAL
35
n
9
VAL
35
B
LYS
36
n
10
LYS
36
B
ASP
37
n
11
ASP
37
B
VAL
38
n
12
VAL
38
B
GLU
39
n
13
GLU
39
B
LEU
40
n
14
LEU
40
B
ASP
41
n
15
ASP
41
B
GLY
42
n
16
GLY
42
B
ARG
43
n
17
ARG
43
B
TRP
44
n
18
TRP
44
B
ASP
45
n
19
ASP
45
B
n
20
46
B
n
21
47
B
n
22
48
B
n
23
49
B
n
24
50
B
n
25
51
B
n
26
52
B
n
27
53
B
ASN
54
n
28
ASN
54
B
CYS
55
n
29
CYS
55
B
PRO
56
n
30
PRO
56
B
ILE
57
n
31
ILE
57
B
THR
58
n
32
THR
58
B
VAL
59
n
33
VAL
59
B
PHE
60
n
34
PHE
60
B
THR
61
n
35
THR
61
B
ASP
62
n
36
ASP
62
B
GLY
63
n
37
GLY
63
B
TYR
64
n
38
TYR
64
B
LEU
65
n
39
LEU
65
B
LEU
66
n
40
LEU
66
B
THR
67
n
41
THR
67
B
LEU
68
n
42
LEU
68
B
LYS
69
n
43
LYS
69
B
ASN
70
n
44
ASN
70
B
ALA
71
n
45
ALA
71
B
SER
72
n
46
SER
72
B
PRO
73
n
47
PRO
73
B
ASP
74
n
48
ASP
74
B
ARG
75
n
49
ARG
75
B
ASP
76
n
50
ASP
76
B
MSE
77
n
51
MSE
77
B
THR
78
n
52
THR
78
B
ILE
79
n
53
ILE
79
B
ARG
80
n
54
ARG
80
B
ILE
81
n
55
ILE
81
B
THR
82
n
56
THR
82
B
ASP
83
n
57
ASP
83
B
MSE
84
n
58
MSE
84
B
ALA
85
n
59
ALA
85
B
LYS
86
n
60
LYS
86
B
GLY
87
n
61
GLY
87
B
GLY
88
n
62
GLY
88
B
VAL
89
n
63
VAL
89
B
VAL
90
n
64
VAL
90
B
TYR
91
n
65
TYR
91
B
GLU
92
n
66
GLU
92
B
ASN
93
n
67
ASN
93
B
ASP
94
n
68
ASP
94
B
ILE
95
n
69
ILE
95
B
PRO
96
n
70
PRO
96
B
GLU
97
n
71
GLU
97
B
VAL
98
n
72
VAL
98
B
GLN
99
n
73
GLN
99
B
SER
100
n
74
SER
100
B
ALA
101
n
75
ALA
101
B
TYR
102
n
76
TYR
102
B
ILE
103
n
77
ILE
103
B
THR
104
n
78
THR
104
B
ILE
105
n
79
ILE
105
B
SER
106
n
80
SER
106
B
ILE
107
n
81
ILE
107
B
ALA
108
n
82
ALA
108
B
ASN
109
n
83
ASN
109
B
PHE
110
n
84
PHE
110
B
PRO
111
n
85
PRO
111
B
ALA
112
n
86
ALA
112
B
GLU
113
n
87
GLU
113
B
GLU
114
n
88
GLU
114
B
TYR
115
n
89
TYR
115
B
LYS
116
n
90
LYS
116
B
LEU
117
n
91
LEU
117
B
GLU
118
n
92
GLU
118
B
ILE
119
n
93
ILE
119
B
THR
120
n
94
THR
120
B
GLY
121
n
95
GLY
121
B
THR
122
n
96
THR
122
B
PRO
123
n
97
PRO
123
B
SER
124
n
98
SER
124
B
GLY
125
n
99
GLY
125
B
HIS
126
n
100
HIS
126
B
LEU
127
n
101
LEU
127
B
THR
128
n
102
THR
128
B
GLY
129
n
103
GLY
129
B
TYR
130
n
104
TYR
130
B
PHE
131
n
105
PHE
131
B
THR
132
n
106
THR
132
B
LYS
133
n
107
LYS
133
B
GLU
134
n
108
GLU
134
B
1.1627
0.3124
0.0569
1.7736
0.0921
2.3912
0.0150
-0.0750
0.0047
0.0108
-0.0250
0.0761
-0.0036
0.0341
0.0100
-0.0637
0.0074
-0.0065
-0.0470
-0.0074
-0.0435
refined
9.2825
11.7246
10.8684
X-RAY DIFFRACTION
1.2694
-0.6028
-0.4287
1.6648
-0.1177
1.9261
-0.0035
0.0804
0.0129
-0.0030
-0.0244
0.0670
0.0434
0.0573
0.0278
-0.0578
-0.0095
0.0037
-0.0388
-0.0125
-0.0292
refined
10.6125
22.0998
-9.3901
X-RAY DIFFRACTION
A
34
A
8
A
134
A
108
X-RAY DIFFRACTION
1
B
34
B
8
B
134
B
108
X-RAY DIFFRACTION
2
author_and_software_defined_assembly
PISA
1
monomeric
author_and_software_defined_assembly
PISA
1
monomeric
gel filtration
gel filtration
A
MSE
77
SELENOMETHIONINE
A
MSE
51
MET
A
MSE
84
SELENOMETHIONINE
A
MSE
58
MET
B
MSE
77
SELENOMETHIONINE
B
MSE
51
MET
B
MSE
84
SELENOMETHIONINE
B
MSE
58
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
LYS
36
A
N
LYS
10
A
O
THR
61
A
O
THR
35
A
N
PHE
60
A
N
PHE
34
A
O
THR
67
A
O
THR
41
A
N
LEU
66
A
N
LEU
40
A
O
ILE
105
A
O
ILE
79
A
N
ARG
43
A
N
ARG
17
A
O
HIS
126
A
O
HIS
100
A
O
GLY
129
A
O
GLY
103
A
N
LEU
117
A
N
LEU
91
A
O
LYS
116
A
O
LYS
90
A
N
THR
82
A
N
THR
56
A
N
MSE
77
A
N
MSE
51
A
O
ILE
95
A
O
ILE
69
B
N
VAL
38
B
N
VAL
12
B
O
VAL
59
B
O
VAL
33
B
N
PHE
60
B
N
PHE
34
B
O
THR
67
B
O
THR
41
B
N
LEU
66
B
N
LEU
40
B
O
ILE
105
B
O
ILE
79
B
N
ARG
43
B
N
ARG
17
B
O
HIS
126
B
O
HIS
100
B
O
PHE
131
B
O
PHE
105
B
N
TYR
115
B
N
TYR
89
B
O
LYS
116
B
O
LYS
90
B
N
THR
82
B
N
THR
56
B
N
ILE
81
B
N
ILE
55
B
O
TYR
91
B
O
TYR
65
1
A
CD
LYS
36
A
CD
LYS
10
1
Y
1
A
CE
LYS
36
A
CE
LYS
10
1
Y
1
A
NZ
LYS
36
A
NZ
LYS
10
1
Y
1
A
CG
ASN
54
A
CG
ASN
28
1
Y
1
A
OD1
ASN
54
A
OD1
ASN
28
1
Y
1
A
ND2
ASN
54
A
ND2
ASN
28
1
Y
1
A
CG
GLU
134
A
CG
GLU
108
1
Y
1
A
CD
GLU
134
A
CD
GLU
108
1
Y
1
A
OE1
GLU
134
A
OE1
GLU
108
1
Y
1
A
OE2
GLU
134
A
OE2
GLU
108
1
Y
1
B
CG
LYS
36
B
CG
LYS
10
1
Y
1
B
CD
LYS
36
B
CD
LYS
10
1
Y
1
B
CE
LYS
36
B
CE
LYS
10
1
Y
1
B
NZ
LYS
36
B
NZ
LYS
10
1
Y
1
B
CD
GLU
39
B
CD
GLU
13
1
Y
1
B
OE1
GLU
39
B
OE1
GLU
13
1
Y
1
B
OE2
GLU
39
B
OE2
GLU
13
1
Y
1
B
CG
ASN
54
B
CG
ASN
28
1
Y
1
B
OD1
ASN
54
B
OD1
ASN
28
1
Y
1
B
ND2
ASN
54
B
ND2
ASN
28
1
Y
1
B
CG
TYR
64
B
CG
TYR
38
1
Y
1
B
CD1
TYR
64
B
CD1
TYR
38
1
Y
1
B
CD2
TYR
64
B
CD2
TYR
38
1
Y
1
B
CE1
TYR
64
B
CE1
TYR
38
1
Y
1
B
CE2
TYR
64
B
CE2
TYR
38
1
Y
1
B
CZ
TYR
64
B
CZ
TYR
38
1
Y
1
B
OH
TYR
64
B
OH
TYR
38
1
Y
1
A
GLY
27
A
GLY
1
1
Y
1
A
ALA
28
A
ALA
2
1
Y
1
A
ASN
29
A
ASN
3
1
Y
1
A
THR
30
A
THR
4
1
Y
1
A
THR
31
A
THR
5
1
Y
1
A
GLU
32
A
GLU
6
1
Y
1
A
THR
33
A
THR
7
1
Y
1
A
PRO
47
A
PRO
21
1
Y
1
A
ILE
48
A
ILE
22
1
Y
1
A
ARG
49
A
ARG
23
1
Y
1
A
SER
50
A
SER
24
1
Y
1
A
ALA
51
A
ALA
25
1
Y
1
A
ALA
52
A
ALA
26
1
Y
1
A
THR
53
A
THR
27
1
Y
1
B
GLY
27
B
GLY
1
1
Y
1
B
ALA
28
B
ALA
2
1
Y
1
B
ASN
29
B
ASN
3
1
Y
1
B
THR
30
B
THR
4
1
Y
1
B
THR
31
B
THR
5
1
Y
1
B
GLU
32
B
GLU
6
1
Y
1
B
THR
33
B
THR
7
1
Y
1
B
ASP
46
B
ASP
20
1
Y
1
B
PRO
47
B
PRO
21
1
Y
1
B
ILE
48
B
ILE
22
1
Y
1
B
ARG
49
B
ARG
23
1
Y
1
B
SER
50
B
SER
24
1
Y
1
B
ALA
51
B
ALA
25
1
Y
1
B
ALA
52
B
ALA
26
1
Y
1
B
THR
53
B
THR
27
1
Y
1
A
ASP
74
-159.09
5.85
1
B
ASP
74
-153.23
6.03
18.342
0.370
0.000
-0.050
0.320
0.000
-0.700
0.965
0.947
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. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
4. THE FOLLOWING REGIONS ARE DISORDERED: A/B0, A/B28-33,
A47-53, B46-53.
0.220
0.174
0.176
1.700
28.677
1283
25099
5.100
99.630
3.951
0.068
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
0.00
SAD
0.098
0.104
0.800
0.800
1.200
MAXIMUM LIKELIHOOD WITH PHASES
MASK
1.700
28.677
283
1722
0
0
1439
0.015
0.022
1532
0.001
0.020
1019
1.494
1.977
2099
0.845
3.000
2516
6.224
5.000
205
41.188
25.156
64
12.758
15.000
259
16.805
15.000
6
0.087
0.200
244
0.006
0.020
1708
0.001
0.020
288
0.193
0.200
235
0.210
0.200
1061
0.175
0.200
712
0.089
0.200
876
0.116
0.200
191
0.134
0.200
10
0.180
0.200
21
0.171
0.200
19
1.914
3.000
1033
0.552
3.000
391
2.717
5.000
1579
4.374
8.000
625
5.982
11.000
509
1
A
1
553
X-RAY DIFFRACTION
MEDIUM POSITIONAL
0.120
0.500
1
A
1
664
X-RAY DIFFRACTION
LOOSE POSITIONAL
0.360
5.000
1
A
1
553
X-RAY DIFFRACTION
MEDIUM THERMAL
0.580
2.000
1
A
1
664
X-RAY DIFFRACTION
LOOSE THERMAL
1.150
10.000
0.365
0.270
1.744
74
1685
1759
20
95.440
24.306
1.70
28.677
3D33
25116
0.098
0.098
1
4.600
7.400
99.600
0.871
1.70
1.74
0.9
12323
1763
0.871
1
7.00
95.70
0.696
1.74
1.79
1.1
13415
1803
0.696
1
7.40
100.00
0.550
1.79
1.84
1.4
13163
1769
0.550
1
7.40
100.00
0.432
1.84
1.90
1.8
12677
1698
0.432
1
7.50
100.00
0.335
1.90
1.96
2.2
12476
1675
0.335
1
7.40
100.00
0.250
1.96
2.03
2.9
11840
1594
0.250
1
7.40
100.00
0.203
2.03
2.11
3.6
11366
1530
0.203
1
7.40
100.00
0.177
2.11
2.19
4.1
11136
1495
0.177
1
7.40
100.00
0.157
2.19
2.29
4.5
10606
1425
0.157
1
7.40
100.00
0.139
2.29
2.40
5.0
10194
1370
0.139
1
7.40
100.00
0.123
2.40
2.53
5.5
9715
1303
0.123
1
7.50
100.00
0.105
2.53
2.69
6.3
9233
1240
0.105
1
7.40
100.00
0.095
2.69
2.87
6.6
8635
1156
0.095
1
7.50
100.00
0.084
2.87
3.10
7.6
8099
1083
0.084
1
7.50
100.00
0.073
3.10
3.40
8.3
7440
996
0.073
1
7.50
100.00
0.067
3.40
3.80
8.7
6694
896
0.067
1
7.50
100.00
0.066
3.80
4.39
8.8
6017
809
0.066
1
7.40
100.00
0.068
4.39
5.38
8.6
5004
681
0.068
1
7.30
100.00
0.072
5.38
7.60
8.7
3807
534
0.072
1
7.10
100.00
0.063
7.60
28.68
9.4
1979
296
0.063
1
6.70
97.20
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
September 10, 2007
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
3.004
data reduction
MOSFLM
Crystal structure of a duf3244 family protein with an immunoglobulin-like beta-sandwich fold (bvu_0276) from bacteroides vulgatus atcc 8482 at 1.70 A resolution
1
N
N
1
N
N
2
N
N
2
N
N
AUTHORS STATE THAT ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY (anSEC) SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
A
PRO
96
A
PRO
70
HELX_P
A
SER
100
A
SER
74
5
1
5
B
PRO
96
B
PRO
70
HELX_P
B
SER
100
B
SER
74
5
2
5
covale
1.339
both
A
ASP
76
A
C
ASP
50
1_555
A
MSE
77
A
N
MSE
51
1_555
covale
1.324
both
A
MSE
77
A
C
MSE
51
1_555
A
THR
78
A
N
THR
52
1_555
covale
1.324
both
A
ASP
83
A
C
ASP
57
1_555
A
MSE
84
A
N
MSE
58
1_555
covale
1.328
both
A
MSE
84
A
C
MSE
58
1_555
A
ALA
85
A
N
ALA
59
1_555
covale
1.332
both
B
ASP
76
B
C
ASP
50
1_555
B
MSE
77
B
N
MSE
51
1_555
covale
1.324
both
B
MSE
77
B
C
MSE
51
1_555
B
THR
78
B
N
THR
52
1_555
covale
1.331
both
B
ASP
83
B
C
ASP
57
1_555
B
MSE
84
B
N
MSE
58
1_555
covale
1.334
both
B
MSE
84
B
C
MSE
58
1_555
B
ALA
85
B
N
ALA
59
1_555
UNKNOWN FUNCTION
Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, unknown function
A
THR
122
A
THR
96
1
A
PRO
123
A
PRO
97
3.66
B
THR
122
B
THR
96
1
B
PRO
123
B
PRO
97
0.49
A
B
A
34
A
PRO
8
A
134
A
GLU
108
5
B
34
B
PRO
8
B
134
B
GLU
108
5
A6KX32_BACV8
UNP
1
28
A6KX32
ANTTETPVKDVELDGRWDDPIRSAATNCPITVFTDGYLLTLKNASPDRDMTIRITDMAKGGVVYENDIPEVQSAYITISI
ANFPAEEYKLEITGTPSGHLTGYFTKE
28
134
3D33
28
134
A6KX32
A
1
2
108
28
134
3D33
28
134
A6KX32
B
1
2
108
1
expression tag
GLY
27
3D33
A
A6KX32
UNP
1
2
expression tag
GLY
27
3D33
B
A6KX32
UNP
1
4
5
4
5
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
LYS
36
A
LYS
10
A
ASP
37
A
ASP
11
A
ILE
57
A
ILE
31
A
ASP
62
A
ASP
36
A
LEU
65
A
LEU
39
A
ASN
70
A
ASN
44
A
TYR
102
A
TYR
76
A
SER
106
A
SER
80
A
ASP
41
A
ASP
15
A
ARG
43
A
ARG
17
A
HIS
126
A
HIS
100
A
LYS
133
A
LYS
107
A
GLU
113
A
GLU
87
A
THR
122
A
THR
96
A
ASP
76
A
ASP
50
A
ASP
83
A
ASP
57
A
VAL
89
A
VAL
63
A
ILE
95
A
ILE
69
B
LYS
36
B
LYS
10
B
VAL
38
B
VAL
12
B
ILE
57
B
ILE
31
B
ASP
62
B
ASP
36
B
LEU
65
B
LEU
39
B
ASN
70
B
ASN
44
B
TYR
102
B
TYR
76
B
SER
106
B
SER
80
B
ASP
41
B
ASP
15
B
ARG
43
B
ARG
17
B
HIS
126
B
HIS
100
B
LYS
133
B
LYS
107
B
GLU
113
B
GLU
87
B
THR
122
B
THR
96
B
ASP
76
B
ASP
50
B
ASP
83
B
ASP
57
B
VAL
89
B
VAL
63
B
ILE
95
B
ILE
69
4
P 1 21 1