0.024850
0.000000
0.008249
0.000000
0.013604
0.000000
0.000000
0.000000
0.019678
0.000000
0.000000
0.000000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
108.360
90.000
40.242
73.507
53.544
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
C6 H8 O7
192.124
CITRIC ACID
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 putative periplasmic protein of unknown function (YP_001299723.1) from Bacteroides vulgatus ATCC 8482 at 1.64 A resolution
10.2210/pdb3elg/pdb
pdb_00003elg
100
1
Flat mirror (vertical focusing)
CCD
2008-08-07
MARMOSAIC 325 mm CCD
Single crystal Si(111) bent monochromator (horizontal focusing)
SINGLE WAVELENGTH
M
x-ray
1
0.97864
1.0
BL11-1
SSRL
0.97864
SYNCHROTRON
SSRL BEAMLINE BL11-1
14596.265
uncharacterized periplasmic protein
2
man
polymer
192.124
CITRIC ACID
1
syn
non-polymer
18.015
water
338
nat
water
no
yes
GAGDVVTRDVNKLPVAARE(MSE)IGKHFSQTKVAYIKIEKDLFQTTSYDVKLADGIELEFNSKGEWLEIDCKNKSVPST
FIPQAISKY(MSE)KANYNGHKTVKIERNRKGYELTLENGLEVDFDQFGGFLKLSD
GAGDVVTRDVNKLPVAAREMIGKHFSQTKVAYIKIEKDLFQTTSYDVKLADGIELEFNSKGEWLEIDCKNKSVPSTFIPQ
AISKYMKANYNGHKTVKIERNRKGYELTLENGLEVDFDQFGGFLKLSD
A,B
390186
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
sample
8482
YP_001299723.1, BVU_2443
435590
Bacteroides vulgatus ATCC 8482
562
Escherichia coli
HK100
Plasmid
SpeedET
1
2.57
52.23
VAPOR DIFFUSION, SITTING DROP
6.0
23.8% polyethylene glycol 3000, 0.1M citric acid pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
277
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
2008-10-14
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
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
RCSB
Y
RCSB
2008-09-22
REL
REL
CIT
CITRIC ACID
HOH
water
SEQUENCE THE CONSTRUCT (RESIDUES 20-146) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
CIT
1
2
CIT
CIT
1
B
HOH
2
3
HOH
HOH
147
A
HOH
3
3
HOH
HOH
148
A
HOH
5
3
HOH
HOH
149
A
HOH
12
3
HOH
HOH
150
A
HOH
16
3
HOH
HOH
151
A
HOH
18
3
HOH
HOH
152
A
HOH
19
3
HOH
HOH
153
A
HOH
20
3
HOH
HOH
154
A
HOH
21
3
HOH
HOH
155
A
HOH
22
3
HOH
HOH
156
A
HOH
23
3
HOH
HOH
157
A
HOH
24
3
HOH
HOH
158
A
HOH
25
3
HOH
HOH
159
A
HOH
26
3
HOH
HOH
160
A
HOH
27
3
HOH
HOH
161
A
HOH
28
3
HOH
HOH
162
A
HOH
29
3
HOH
HOH
163
A
HOH
30
3
HOH
HOH
164
A
HOH
31
3
HOH
HOH
165
A
HOH
32
3
HOH
HOH
166
A
HOH
33
3
HOH
HOH
167
A
HOH
34
3
HOH
HOH
168
A
HOH
35
3
HOH
HOH
169
A
HOH
36
3
HOH
HOH
170
A
HOH
37
3
HOH
HOH
171
A
HOH
38
3
HOH
HOH
172
A
HOH
39
3
HOH
HOH
173
A
HOH
40
3
HOH
HOH
174
A
HOH
41
3
HOH
HOH
175
A
HOH
42
3
HOH
HOH
176
A
HOH
43
3
HOH
HOH
177
A
HOH
44
3
HOH
HOH
178
A
HOH
45
3
HOH
HOH
179
A
HOH
46
3
HOH
HOH
180
A
HOH
47
3
HOH
HOH
181
A
HOH
48
3
HOH
HOH
182
A
HOH
49
3
HOH
HOH
183
A
HOH
50
3
HOH
HOH
184
A
HOH
51
3
HOH
HOH
185
A
HOH
52
3
HOH
HOH
186
A
HOH
53
3
HOH
HOH
187
A
HOH
54
3
HOH
HOH
188
A
HOH
55
3
HOH
HOH
189
A
HOH
56
3
HOH
HOH
190
A
HOH
57
3
HOH
HOH
191
A
HOH
58
3
HOH
HOH
192
A
HOH
59
3
HOH
HOH
193
A
HOH
60
3
HOH
HOH
194
A
HOH
61
3
HOH
HOH
195
A
HOH
62
3
HOH
HOH
196
A
HOH
63
3
HOH
HOH
197
A
HOH
64
3
HOH
HOH
198
A
HOH
65
3
HOH
HOH
199
A
HOH
66
3
HOH
HOH
200
A
HOH
67
3
HOH
HOH
201
A
HOH
68
3
HOH
HOH
202
A
HOH
69
3
HOH
HOH
203
A
HOH
70
3
HOH
HOH
204
A
HOH
71
3
HOH
HOH
205
A
HOH
72
3
HOH
HOH
206
A
HOH
73
3
HOH
HOH
207
A
HOH
74
3
HOH
HOH
208
A
HOH
75
3
HOH
HOH
209
A
HOH
76
3
HOH
HOH
210
A
HOH
77
3
HOH
HOH
211
A
HOH
78
3
HOH
HOH
212
A
HOH
79
3
HOH
HOH
213
A
HOH
80
3
HOH
HOH
214
A
HOH
81
3
HOH
HOH
215
A
HOH
82
3
HOH
HOH
216
A
HOH
83
3
HOH
HOH
217
A
HOH
84
3
HOH
HOH
218
A
HOH
85
3
HOH
HOH
219
A
HOH
86
3
HOH
HOH
220
A
HOH
87
3
HOH
HOH
221
A
HOH
88
3
HOH
HOH
222
A
HOH
89
3
HOH
HOH
223
A
HOH
90
3
HOH
HOH
224
A
HOH
91
3
HOH
HOH
225
A
HOH
92
3
HOH
HOH
226
A
HOH
93
3
HOH
HOH
227
A
HOH
94
3
HOH
HOH
228
A
HOH
95
3
HOH
HOH
229
A
HOH
96
3
HOH
HOH
230
A
HOH
97
3
HOH
HOH
231
A
HOH
98
3
HOH
HOH
232
A
HOH
99
3
HOH
HOH
233
A
HOH
100
3
HOH
HOH
234
A
HOH
101
3
HOH
HOH
235
A
HOH
102
3
HOH
HOH
236
A
HOH
103
3
HOH
HOH
237
A
HOH
104
3
HOH
HOH
238
A
HOH
105
3
HOH
HOH
239
A
HOH
106
3
HOH
HOH
240
A
HOH
107
3
HOH
HOH
241
A
HOH
108
3
HOH
HOH
242
A
HOH
109
3
HOH
HOH
243
A
HOH
110
3
HOH
HOH
244
A
HOH
111
3
HOH
HOH
245
A
HOH
112
3
HOH
HOH
246
A
HOH
113
3
HOH
HOH
247
A
HOH
114
3
HOH
HOH
248
A
HOH
115
3
HOH
HOH
249
A
HOH
116
3
HOH
HOH
250
A
HOH
117
3
HOH
HOH
251
A
HOH
118
3
HOH
HOH
252
A
HOH
119
3
HOH
HOH
253
A
HOH
120
3
HOH
HOH
254
A
HOH
121
3
HOH
HOH
255
A
HOH
122
3
HOH
HOH
256
A
HOH
123
3
HOH
HOH
257
A
HOH
124
3
HOH
HOH
258
A
HOH
125
3
HOH
HOH
259
A
HOH
126
3
HOH
HOH
260
A
HOH
127
3
HOH
HOH
261
A
HOH
128
3
HOH
HOH
262
A
HOH
129
3
HOH
HOH
263
A
HOH
130
3
HOH
HOH
264
A
HOH
131
3
HOH
HOH
265
A
HOH
132
3
HOH
HOH
266
A
HOH
133
3
HOH
HOH
267
A
HOH
134
3
HOH
HOH
268
A
HOH
135
3
HOH
HOH
269
A
HOH
136
3
HOH
HOH
270
A
HOH
137
3
HOH
HOH
271
A
HOH
138
3
HOH
HOH
272
A
HOH
139
3
HOH
HOH
273
A
HOH
140
3
HOH
HOH
274
A
HOH
141
3
HOH
HOH
275
A
HOH
142
3
HOH
HOH
276
A
HOH
143
3
HOH
HOH
277
A
HOH
144
3
HOH
HOH
278
A
HOH
145
3
HOH
HOH
279
A
HOH
146
3
HOH
HOH
280
A
HOH
147
3
HOH
HOH
281
A
HOH
148
3
HOH
HOH
282
A
HOH
150
3
HOH
HOH
283
A
HOH
151
3
HOH
HOH
284
A
HOH
152
3
HOH
HOH
285
A
HOH
153
3
HOH
HOH
286
A
HOH
155
3
HOH
HOH
287
A
HOH
157
3
HOH
HOH
288
A
HOH
158
3
HOH
HOH
289
A
HOH
159
3
HOH
HOH
290
A
HOH
160
3
HOH
HOH
291
A
HOH
162
3
HOH
HOH
292
A
HOH
164
3
HOH
HOH
293
A
HOH
166
3
HOH
HOH
294
A
HOH
167
3
HOH
HOH
295
A
HOH
172
3
HOH
HOH
296
A
HOH
173
3
HOH
HOH
297
A
HOH
175
3
HOH
HOH
298
A
HOH
176
3
HOH
HOH
299
A
HOH
177
3
HOH
HOH
300
A
HOH
178
3
HOH
HOH
301
A
HOH
179
3
HOH
HOH
302
A
HOH
182
3
HOH
HOH
303
A
HOH
186
3
HOH
HOH
304
A
HOH
188
3
HOH
HOH
305
A
HOH
189
3
HOH
HOH
306
A
HOH
190
3
HOH
HOH
307
A
HOH
195
3
HOH
HOH
308
A
HOH
196
3
HOH
HOH
309
A
HOH
197
3
HOH
HOH
310
A
HOH
198
3
HOH
HOH
311
A
HOH
199
3
HOH
HOH
312
A
HOH
202
3
HOH
HOH
313
A
HOH
203
3
HOH
HOH
314
A
HOH
205
3
HOH
HOH
315
A
HOH
206
3
HOH
HOH
316
A
HOH
211
3
HOH
HOH
317
A
HOH
213
3
HOH
HOH
318
A
HOH
219
3
HOH
HOH
319
A
HOH
220
3
HOH
HOH
320
A
HOH
225
3
HOH
HOH
321
A
HOH
226
3
HOH
HOH
322
A
HOH
227
3
HOH
HOH
323
A
HOH
228
3
HOH
HOH
324
A
HOH
229
3
HOH
HOH
325
A
HOH
230
3
HOH
HOH
326
A
HOH
231
3
HOH
HOH
327
A
HOH
234
3
HOH
HOH
328
A
HOH
238
3
HOH
HOH
329
A
HOH
239
3
HOH
HOH
330
A
HOH
242
3
HOH
HOH
331
A
HOH
243
3
HOH
HOH
332
A
HOH
257
3
HOH
HOH
333
A
HOH
258
3
HOH
HOH
334
A
HOH
265
3
HOH
HOH
335
A
HOH
266
3
HOH
HOH
336
A
HOH
267
3
HOH
HOH
337
A
HOH
268
3
HOH
HOH
338
A
HOH
269
3
HOH
HOH
339
A
HOH
270
3
HOH
HOH
340
A
HOH
271
3
HOH
HOH
341
A
HOH
272
3
HOH
HOH
342
A
HOH
273
3
HOH
HOH
343
A
HOH
274
3
HOH
HOH
344
A
HOH
275
3
HOH
HOH
345
A
HOH
276
3
HOH
HOH
346
A
HOH
278
3
HOH
HOH
347
A
HOH
279
3
HOH
HOH
348
A
HOH
283
3
HOH
HOH
349
A
HOH
284
3
HOH
HOH
350
A
HOH
285
3
HOH
HOH
351
A
HOH
286
3
HOH
HOH
352
A
HOH
287
3
HOH
HOH
353
A
HOH
288
3
HOH
HOH
354
A
HOH
293
3
HOH
HOH
355
A
HOH
294
3
HOH
HOH
356
A
HOH
295
3
HOH
HOH
357
A
HOH
296
3
HOH
HOH
358
A
HOH
297
3
HOH
HOH
359
A
HOH
298
3
HOH
HOH
360
A
HOH
299
3
HOH
HOH
361
A
HOH
300
3
HOH
HOH
362
A
HOH
301
3
HOH
HOH
363
A
HOH
305
3
HOH
HOH
364
A
HOH
308
3
HOH
HOH
365
A
HOH
310
3
HOH
HOH
366
A
HOH
311
3
HOH
HOH
367
A
HOH
313
3
HOH
HOH
368
A
HOH
316
3
HOH
HOH
369
A
HOH
317
3
HOH
HOH
370
A
HOH
323
3
HOH
HOH
371
A
HOH
324
3
HOH
HOH
372
A
HOH
327
3
HOH
HOH
373
A
HOH
328
3
HOH
HOH
374
A
HOH
329
3
HOH
HOH
375
A
HOH
330
3
HOH
HOH
376
A
HOH
331
3
HOH
HOH
377
A
HOH
332
3
HOH
HOH
378
A
HOH
338
3
HOH
HOH
379
A
HOH
4
3
HOH
HOH
4
B
HOH
6
3
HOH
HOH
6
B
HOH
7
3
HOH
HOH
7
B
HOH
8
3
HOH
HOH
8
B
HOH
9
3
HOH
HOH
9
B
HOH
10
3
HOH
HOH
10
B
HOH
11
3
HOH
HOH
11
B
HOH
13
3
HOH
HOH
13
B
HOH
14
3
HOH
HOH
14
B
HOH
15
3
HOH
HOH
15
B
HOH
17
3
HOH
HOH
17
B
HOH
149
3
HOH
HOH
149
B
HOH
154
3
HOH
HOH
154
B
HOH
156
3
HOH
HOH
156
B
HOH
161
3
HOH
HOH
161
B
HOH
163
3
HOH
HOH
163
B
HOH
165
3
HOH
HOH
165
B
HOH
168
3
HOH
HOH
168
B
HOH
169
3
HOH
HOH
169
B
HOH
170
3
HOH
HOH
170
B
HOH
171
3
HOH
HOH
171
B
HOH
174
3
HOH
HOH
174
B
HOH
180
3
HOH
HOH
180
B
HOH
181
3
HOH
HOH
181
B
HOH
183
3
HOH
HOH
183
B
HOH
184
3
HOH
HOH
184
B
HOH
185
3
HOH
HOH
185
B
HOH
187
3
HOH
HOH
187
B
HOH
191
3
HOH
HOH
191
B
HOH
192
3
HOH
HOH
192
B
HOH
193
3
HOH
HOH
193
B
HOH
194
3
HOH
HOH
194
B
HOH
200
3
HOH
HOH
200
B
HOH
201
3
HOH
HOH
201
B
HOH
204
3
HOH
HOH
204
B
HOH
207
3
HOH
HOH
207
B
HOH
208
3
HOH
HOH
208
B
HOH
209
3
HOH
HOH
209
B
HOH
210
3
HOH
HOH
210
B
HOH
212
3
HOH
HOH
212
B
HOH
214
3
HOH
HOH
214
B
HOH
215
3
HOH
HOH
215
B
HOH
216
3
HOH
HOH
216
B
HOH
217
3
HOH
HOH
217
B
HOH
218
3
HOH
HOH
218
B
HOH
222
3
HOH
HOH
222
B
HOH
223
3
HOH
HOH
223
B
HOH
224
3
HOH
HOH
224
B
HOH
232
3
HOH
HOH
232
B
HOH
233
3
HOH
HOH
233
B
HOH
235
3
HOH
HOH
235
B
HOH
236
3
HOH
HOH
236
B
HOH
237
3
HOH
HOH
237
B
HOH
240
3
HOH
HOH
240
B
HOH
241
3
HOH
HOH
241
B
HOH
244
3
HOH
HOH
244
B
HOH
245
3
HOH
HOH
245
B
HOH
246
3
HOH
HOH
246
B
HOH
247
3
HOH
HOH
247
B
HOH
248
3
HOH
HOH
248
B
HOH
249
3
HOH
HOH
249
B
HOH
250
3
HOH
HOH
250
B
HOH
251
3
HOH
HOH
251
B
HOH
252
3
HOH
HOH
252
B
HOH
253
3
HOH
HOH
253
B
HOH
254
3
HOH
HOH
254
B
HOH
255
3
HOH
HOH
255
B
HOH
256
3
HOH
HOH
256
B
HOH
259
3
HOH
HOH
259
B
HOH
260
3
HOH
HOH
260
B
HOH
261
3
HOH
HOH
261
B
HOH
262
3
HOH
HOH
262
B
HOH
263
3
HOH
HOH
263
B
HOH
264
3
HOH
HOH
264
B
HOH
277
3
HOH
HOH
277
B
HOH
280
3
HOH
HOH
280
B
HOH
281
3
HOH
HOH
281
B
HOH
282
3
HOH
HOH
282
B
HOH
289
3
HOH
HOH
289
B
HOH
290
3
HOH
HOH
290
B
HOH
291
3
HOH
HOH
291
B
HOH
292
3
HOH
HOH
292
B
HOH
302
3
HOH
HOH
302
B
HOH
303
3
HOH
HOH
303
B
HOH
304
3
HOH
HOH
304
B
HOH
306
3
HOH
HOH
306
B
HOH
307
3
HOH
HOH
307
B
HOH
309
3
HOH
HOH
309
B
HOH
312
3
HOH
HOH
312
B
HOH
314
3
HOH
HOH
314
B
HOH
315
3
HOH
HOH
315
B
HOH
318
3
HOH
HOH
318
B
HOH
319
3
HOH
HOH
319
B
HOH
320
3
HOH
HOH
320
B
HOH
321
3
HOH
HOH
321
B
HOH
322
3
HOH
HOH
322
B
HOH
325
3
HOH
HOH
325
B
HOH
326
3
HOH
HOH
326
B
HOH
333
3
HOH
HOH
333
B
HOH
334
3
HOH
HOH
334
B
HOH
335
3
HOH
HOH
335
B
HOH
336
3
HOH
HOH
336
B
HOH
337
3
HOH
HOH
337
B
HOH
339
3
HOH
HOH
339
B
HOH
340
3
HOH
HOH
340
B
n
1
19
A
ALA
20
n
2
ALA
20
A
GLY
21
n
3
GLY
21
A
ASP
22
n
4
ASP
22
A
VAL
23
n
5
VAL
23
A
VAL
24
n
6
VAL
24
A
THR
25
n
7
THR
25
A
ARG
26
n
8
ARG
26
A
ASP
27
n
9
ASP
27
A
VAL
28
n
10
VAL
28
A
ASN
29
n
11
ASN
29
A
LYS
30
n
12
LYS
30
A
LEU
31
n
13
LEU
31
A
PRO
32
n
14
PRO
32
A
VAL
33
n
15
VAL
33
A
ALA
34
n
16
ALA
34
A
ALA
35
n
17
ALA
35
A
ARG
36
n
18
ARG
36
A
GLU
37
n
19
GLU
37
A
MSE
38
n
20
MSE
38
A
ILE
39
n
21
ILE
39
A
GLY
40
n
22
GLY
40
A
LYS
41
n
23
LYS
41
A
HIS
42
n
24
HIS
42
A
PHE
43
n
25
PHE
43
A
SER
44
n
26
SER
44
A
GLN
45
n
27
GLN
45
A
THR
46
n
28
THR
46
A
LYS
47
n
29
LYS
47
A
VAL
48
n
30
VAL
48
A
ALA
49
n
31
ALA
49
A
TYR
50
n
32
TYR
50
A
ILE
51
n
33
ILE
51
A
LYS
52
n
34
LYS
52
A
ILE
53
n
35
ILE
53
A
GLU
54
n
36
GLU
54
A
LYS
55
n
37
LYS
55
A
ASP
56
n
38
ASP
56
A
LEU
57
n
39
LEU
57
A
PHE
58
n
40
PHE
58
A
GLN
59
n
41
GLN
59
A
THR
60
n
42
THR
60
A
THR
61
n
43
THR
61
A
SER
62
n
44
SER
62
A
TYR
63
n
45
TYR
63
A
ASP
64
n
46
ASP
64
A
VAL
65
n
47
VAL
65
A
LYS
66
n
48
LYS
66
A
LEU
67
n
49
LEU
67
A
ALA
68
n
50
ALA
68
A
ASP
69
n
51
ASP
69
A
GLY
70
n
52
GLY
70
A
ILE
71
n
53
ILE
71
A
GLU
72
n
54
GLU
72
A
LEU
73
n
55
LEU
73
A
GLU
74
n
56
GLU
74
A
PHE
75
n
57
PHE
75
A
ASN
76
n
58
ASN
76
A
SER
77
n
59
SER
77
A
LYS
78
n
60
LYS
78
A
GLY
79
n
61
GLY
79
A
GLU
80
n
62
GLU
80
A
TRP
81
n
63
TRP
81
A
LEU
82
n
64
LEU
82
A
GLU
83
n
65
GLU
83
A
ILE
84
n
66
ILE
84
A
ASP
85
n
67
ASP
85
A
CYS
86
n
68
CYS
86
A
LYS
87
n
69
LYS
87
A
ASN
88
n
70
ASN
88
A
LYS
89
n
71
LYS
89
A
SER
90
n
72
SER
90
A
VAL
91
n
73
VAL
91
A
PRO
92
n
74
PRO
92
A
SER
93
n
75
SER
93
A
THR
94
n
76
THR
94
A
PHE
95
n
77
PHE
95
A
ILE
96
n
78
ILE
96
A
PRO
97
n
79
PRO
97
A
GLN
98
n
80
GLN
98
A
ALA
99
n
81
ALA
99
A
ILE
100
n
82
ILE
100
A
SER
101
n
83
SER
101
A
LYS
102
n
84
LYS
102
A
TYR
103
n
85
TYR
103
A
MSE
104
n
86
MSE
104
A
LYS
105
n
87
LYS
105
A
ALA
106
n
88
ALA
106
A
ASN
107
n
89
ASN
107
A
TYR
108
n
90
TYR
108
A
ASN
109
n
91
ASN
109
A
GLY
110
n
92
GLY
110
A
HIS
111
n
93
HIS
111
A
LYS
112
n
94
LYS
112
A
THR
113
n
95
THR
113
A
VAL
114
n
96
VAL
114
A
LYS
115
n
97
LYS
115
A
ILE
116
n
98
ILE
116
A
GLU
117
n
99
GLU
117
A
ARG
118
n
100
ARG
118
A
ASN
119
n
101
ASN
119
A
ARG
120
n
102
ARG
120
A
LYS
121
n
103
LYS
121
A
GLY
122
n
104
GLY
122
A
TYR
123
n
105
TYR
123
A
GLU
124
n
106
GLU
124
A
LEU
125
n
107
LEU
125
A
THR
126
n
108
THR
126
A
LEU
127
n
109
LEU
127
A
GLU
128
n
110
GLU
128
A
ASN
129
n
111
ASN
129
A
GLY
130
n
112
GLY
130
A
LEU
131
n
113
LEU
131
A
GLU
132
n
114
GLU
132
A
VAL
133
n
115
VAL
133
A
ASP
134
n
116
ASP
134
A
PHE
135
n
117
PHE
135
A
ASP
136
n
118
ASP
136
A
GLN
137
n
119
GLN
137
A
PHE
138
n
120
PHE
138
A
GLY
139
n
121
GLY
139
A
GLY
140
n
122
GLY
140
A
PHE
141
n
123
PHE
141
A
LEU
142
n
124
LEU
142
A
LYS
143
n
125
LYS
143
A
LEU
144
n
126
LEU
144
A
SER
145
n
127
SER
145
A
ASP
146
n
128
ASP
146
A
n
1
19
B
n
2
20
B
GLY
21
n
3
GLY
21
B
ASP
22
n
4
ASP
22
B
VAL
23
n
5
VAL
23
B
VAL
24
n
6
VAL
24
B
THR
25
n
7
THR
25
B
ARG
26
n
8
ARG
26
B
ASP
27
n
9
ASP
27
B
VAL
28
n
10
VAL
28
B
ASN
29
n
11
ASN
29
B
LYS
30
n
12
LYS
30
B
LEU
31
n
13
LEU
31
B
PRO
32
n
14
PRO
32
B
VAL
33
n
15
VAL
33
B
ALA
34
n
16
ALA
34
B
ALA
35
n
17
ALA
35
B
ARG
36
n
18
ARG
36
B
GLU
37
n
19
GLU
37
B
MSE
38
n
20
MSE
38
B
ILE
39
n
21
ILE
39
B
GLY
40
n
22
GLY
40
B
LYS
41
n
23
LYS
41
B
HIS
42
n
24
HIS
42
B
PHE
43
n
25
PHE
43
B
SER
44
n
26
SER
44
B
GLN
45
n
27
GLN
45
B
THR
46
n
28
THR
46
B
LYS
47
n
29
LYS
47
B
VAL
48
n
30
VAL
48
B
ALA
49
n
31
ALA
49
B
TYR
50
n
32
TYR
50
B
ILE
51
n
33
ILE
51
B
LYS
52
n
34
LYS
52
B
ILE
53
n
35
ILE
53
B
GLU
54
n
36
GLU
54
B
LYS
55
n
37
LYS
55
B
ASP
56
n
38
ASP
56
B
LEU
57
n
39
LEU
57
B
PHE
58
n
40
PHE
58
B
GLN
59
n
41
GLN
59
B
THR
60
n
42
THR
60
B
THR
61
n
43
THR
61
B
SER
62
n
44
SER
62
B
TYR
63
n
45
TYR
63
B
ASP
64
n
46
ASP
64
B
VAL
65
n
47
VAL
65
B
LYS
66
n
48
LYS
66
B
LEU
67
n
49
LEU
67
B
ALA
68
n
50
ALA
68
B
ASP
69
n
51
ASP
69
B
GLY
70
n
52
GLY
70
B
ILE
71
n
53
ILE
71
B
GLU
72
n
54
GLU
72
B
LEU
73
n
55
LEU
73
B
GLU
74
n
56
GLU
74
B
PHE
75
n
57
PHE
75
B
ASN
76
n
58
ASN
76
B
SER
77
n
59
SER
77
B
LYS
78
n
60
LYS
78
B
GLY
79
n
61
GLY
79
B
GLU
80
n
62
GLU
80
B
TRP
81
n
63
TRP
81
B
LEU
82
n
64
LEU
82
B
GLU
83
n
65
GLU
83
B
ILE
84
n
66
ILE
84
B
ASP
85
n
67
ASP
85
B
CYS
86
n
68
CYS
86
B
LYS
87
n
69
LYS
87
B
ASN
88
n
70
ASN
88
B
LYS
89
n
71
LYS
89
B
SER
90
n
72
SER
90
B
VAL
91
n
73
VAL
91
B
PRO
92
n
74
PRO
92
B
SER
93
n
75
SER
93
B
THR
94
n
76
THR
94
B
PHE
95
n
77
PHE
95
B
ILE
96
n
78
ILE
96
B
PRO
97
n
79
PRO
97
B
GLN
98
n
80
GLN
98
B
ALA
99
n
81
ALA
99
B
ILE
100
n
82
ILE
100
B
SER
101
n
83
SER
101
B
LYS
102
n
84
LYS
102
B
TYR
103
n
85
TYR
103
B
MSE
104
n
86
MSE
104
B
LYS
105
n
87
LYS
105
B
ALA
106
n
88
ALA
106
B
ASN
107
n
89
ASN
107
B
TYR
108
n
90
TYR
108
B
ASN
109
n
91
ASN
109
B
GLY
110
n
92
GLY
110
B
HIS
111
n
93
HIS
111
B
LYS
112
n
94
LYS
112
B
THR
113
n
95
THR
113
B
VAL
114
n
96
VAL
114
B
LYS
115
n
97
LYS
115
B
ILE
116
n
98
ILE
116
B
GLU
117
n
99
GLU
117
B
ARG
118
n
100
ARG
118
B
ASN
119
n
101
ASN
119
B
ARG
120
n
102
ARG
120
B
LYS
121
n
103
LYS
121
B
GLY
122
n
104
GLY
122
B
TYR
123
n
105
TYR
123
B
GLU
124
n
106
GLU
124
B
LEU
125
n
107
LEU
125
B
THR
126
n
108
THR
126
B
LEU
127
n
109
LEU
127
B
GLU
128
n
110
GLU
128
B
ASN
129
n
111
ASN
129
B
GLY
130
n
112
GLY
130
B
LEU
131
n
113
LEU
131
B
GLU
132
n
114
GLU
132
B
VAL
133
n
115
VAL
133
B
ASP
134
n
116
ASP
134
B
PHE
135
n
117
PHE
135
B
ASP
136
n
118
ASP
136
B
GLN
137
n
119
GLN
137
B
PHE
138
n
120
PHE
138
B
GLY
139
n
121
GLY
139
B
GLY
140
n
122
GLY
140
B
PHE
141
n
123
PHE
141
B
LEU
142
n
124
LEU
142
B
LYS
143
n
125
LYS
143
B
LEU
144
n
126
LEU
144
B
SER
145
n
127
SER
145
B
ASP
146
n
128
ASP
146
B
0.7683
-0.6482
-0.3143
1.3105
0.3145
0.9140
-0.0354
-0.0237
-0.0246
0.0008
-0.0074
0.0102
-0.0013
0.0875
0.0428
-0.0431
-0.0031
-0.0130
-0.0280
-0.0001
-0.0315
refined
9.9995
10.2054
8.9038
X-RAY DIFFRACTION
0.8799
0.5101
-0.0073
0.8124
-0.5894
0.8921
0.0921
0.0105
0.0634
0.0248
-0.0897
-0.0774
-0.0481
0.0426
-0.0023
-0.0086
0.0081
0.0231
-0.0370
0.0079
-0.0190
refined
-1.6893
8.2553
-13.1102
X-RAY DIFFRACTION
A
20
A
146
X-RAY DIFFRACTION
1
B
21
B
146
X-RAY DIFFRACTION
2
author_and_software_defined_assembly
PISA
1
monomeric
author_and_software_defined_assembly
PISA
1
monomeric
A
MSE
38
SELENOMETHIONINE
A
MSE
20
MET
A
MSE
104
SELENOMETHIONINE
A
MSE
86
MET
B
MSE
38
SELENOMETHIONINE
B
MSE
20
MET
B
MSE
104
SELENOMETHIONINE
B
MSE
86
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
VAL
23
A
N
VAL
5
A
O
ILE
53
A
O
ILE
35
A
N
ALA
49
A
N
ALA
31
A
O
LYS
66
A
O
LYS
48
A
N
VAL
65
A
N
VAL
47
A
O
LEU
73
A
O
LEU
55
A
N
GLU
72
A
N
GLU
54
A
O
ASP
85
A
O
ASP
67
A
N
ILE
84
A
N
ILE
66
A
O
ILE
116
A
O
ILE
98
A
N
LYS
115
A
N
LYS
97
A
O
THR
126
A
O
THR
108
A
N
LEU
125
A
N
LEU
107
A
O
VAL
133
A
O
VAL
115
A
N
ASP
134
A
N
ASP
116
A
O
LEU
142
A
O
LEU
124
B
N
VAL
23
B
N
VAL
5
B
O
ILE
53
B
O
ILE
35
B
N
LYS
52
B
N
LYS
34
B
O
ASP
64
B
O
ASP
46
B
N
VAL
65
B
N
VAL
47
B
O
LEU
73
B
O
LEU
55
B
N
GLU
74
B
N
GLU
56
B
O
LEU
82
B
O
LEU
64
B
N
ILE
84
B
N
ILE
66
B
O
ILE
116
B
O
ILE
98
B
N
ASN
119
B
N
ASN
101
B
O
GLY
122
B
O
GLY
104
B
N
LEU
125
B
N
LEU
107
B
O
VAL
133
B
O
VAL
115
B
N
ASP
134
B
N
ASP
116
B
O
LYS
143
B
O
LYS
125
1
A
CE
LYS
30
A
CE
LYS
12
1
Y
1
A
NZ
LYS
30
A
NZ
LYS
12
1
Y
1
A
CE
LYS
47
A
CE
LYS
29
1
Y
1
A
NZ
LYS
47
A
NZ
LYS
29
1
Y
1
A
NZ
LYS
52
A
NZ
LYS
34
1
Y
1
A
NZ
LYS
55
A
NZ
LYS
37
1
Y
1
A
CE
LYS
89
A
CE
LYS
71
1
Y
1
A
NZ
LYS
89
A
NZ
LYS
71
1
Y
1
A
CD
GLN
98
A
CD
GLN
80
1
Y
1
A
OE1
GLN
98
A
OE1
GLN
80
1
Y
1
A
NE2
GLN
98
A
NE2
GLN
80
1
Y
1
A
CE
LYS
105
A
CE
LYS
87
1
Y
1
A
NZ
LYS
105
A
NZ
LYS
87
1
Y
1
B
CE
LYS
47
B
CE
LYS
29
1
Y
1
B
NZ
LYS
47
B
NZ
LYS
29
1
Y
1
B
NZ
LYS
55
B
NZ
LYS
37
1
Y
1
B
CD
LYS
89
B
CD
LYS
71
1
Y
1
B
CE
LYS
89
B
CE
LYS
71
1
Y
1
B
NZ
LYS
89
B
NZ
LYS
71
1
Y
1
B
CD
GLN
98
B
CD
GLN
80
1
Y
1
B
OE1
GLN
98
B
OE1
GLN
80
1
Y
1
B
NE2
GLN
98
B
NE2
GLN
80
1
Y
1
B
CE
LYS
102
B
CE
LYS
84
1
Y
1
B
NZ
LYS
102
B
NZ
LYS
84
1
Y
1
B
CE
LYS
105
B
CE
LYS
87
1
Y
1
B
NZ
LYS
105
B
NZ
LYS
87
1
Y
1
B
CE
LYS
112
B
CE
LYS
94
1
Y
1
B
NZ
LYS
112
B
NZ
LYS
94
1
Y
1
A
GLY
19
A
GLY
1
1
Y
1
B
GLY
19
B
GLY
1
1
Y
1
B
ALA
20
B
ALA
2
1
Y
1
A
LYS
87
67.04
-92.87
1
A
SER
145
A
-147.72
-153.37
1
B
LYS
87
71.62
-96.36
62.67
22.186
8.56
0.490
0.000
0.500
0.080
0.000
-0.250
0.964
0.949
(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
TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL
S-MET INCORPORATION.
(3). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
(4). ONE CITRATE (CIT) ION WAS MODELED BASED ON CRYSTALLIZATION
AND CONCLUSIVE ELECTRON DENSITY.
(5). RAMACHANDRAN OUTLIERS OF LYS 87 IN BOTH A AND B SUBUNITS ARE
SUPPORTED BY ELECTRON DENSITY.
0.209
0.172
0.174
1.640
29.775
1784
35686
5.000
98.150
1.00
0.50
3.741
0.065
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
0.00
SAD
0.096
0.097
0.800
0.800
1.200
MAXIMUM LIKELIHOOD WITH PHASES
MASK
1.640
29.775
338
2352
13
0
2001
0.016
0.022
2302
0.002
0.020
1558
1.506
1.967
3143
1.401
3.000
3847
5.526
5.000
305
34.123
25.727
110
12.723
15.000
426
6.609
15.000
8
0.091
0.200
332
0.007
0.020
2717
0.003
0.020
461
1.774
3.000
1415
0.546
3.000
570
2.938
5.000
2322
4.947
8.000
887
7.518
11.000
821
0.332
0.259
1.682
136
2473
2609
20
96.770
20.084
1.64
29.775
3ELG
35714
0.094
0.094
1
5.959
7.300
98.400
0.865
1.64
1.68
0.9
10044
2621
0.865
1
3.80
97.20
0.791
1.68
1.73
0.9
17773
2522
0.791
1
7.00
97.30
0.638
1.73
1.78
1.2
18925
2468
0.638
1
7.70
97.30
0.471
1.78
1.83
1.6
18383
2397
0.471
1
7.70
97.90
0.370
1.83
1.89
2.0
17900
2333
0.370
1
7.70
98.00
0.286
1.89
1.96
2.6
17369
2268
0.286
1
7.70
97.80
0.211
1.96
2.03
3.6
16885
2203
0.211
1
7.70
98.40
0.182
2.03
2.12
4.0
16179
2112
0.182
1
7.70
98.40
0.139
2.12
2.21
5.3
15687
2040
0.139
1
7.70
98.50
0.130
2.21
2.32
5.3
14767
1931
0.130
1
7.60
98.60
0.111
2.32
2.44
6.6
14123
1841
0.111
1
7.70
99.00
0.098
2.44
2.59
7.3
13473
1753
0.098
1
7.70
98.90
0.090
2.59
2.77
7.5
12690
1656
0.090
1
7.70
99.10
0.077
2.77
2.99
9.0
11886
1555
0.077
1
7.60
99.20
0.065
2.99
3.28
10.2
10850
1418
0.065
1
7.70
99.50
0.058
3.28
3.67
11.3
9912
1303
0.058
1
7.60
99.50
0.056
3.67
4.23
11.2
8638
1135
0.056
1
7.60
99.70
0.048
4.23
5.19
12.7
7350
976
0.048
1
7.50
99.70
0.060
5.19
7.33
10.9
5649
760
0.060
1
7.40
99.70
0.056
7.33
29.80
11.7
3014
422
0.056
1
7.10
97.90
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
5.4.0069
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
program
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 R. Evans
pre@mrc-lmb.cam.ac.uk
5/04/2004
Fortran_77
http://www.ccp4.ac.uk/dist/html/scala.html
SCALA
other
3.2.5
data extraction
PDB
help@deposit.rcsb.org
June 11, 2008
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.006
data reduction
MOSFLM
Crystal structure of a putative periplasmic protein of unknown function (bvu_2443) from bacteroides vulgatus atcc 8482 at 1.64 A resolution
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
A
ASP
27
A
ASP
9
HELX_P
A
LEU
31
A
LEU
13
5
1
5
A
PRO
32
A
PRO
14
HELX_P
A
PHE
43
A
PHE
25
1
2
12
A
PRO
92
A
PRO
74
HELX_P
A
ILE
96
A
ILE
78
5
3
5
A
PRO
97
A
PRO
79
HELX_P
A
TYR
108
A
TYR
90
1
4
12
B
ASP
27
B
ASP
9
HELX_P
B
LEU
31
B
LEU
13
5
5
5
B
PRO
32
B
PRO
14
HELX_P
B
PHE
43
B
PHE
25
1
6
12
B
PRO
92
B
PRO
74
HELX_P
B
ILE
96
B
ILE
78
5
7
5
B
PRO
97
B
PRO
79
HELX_P
B
ASN
109
B
ASN
91
1
8
13
covale
1.333
both
A
A
GLU
37
A
C
GLU
19
1_555
A
MSE
38
A
N
MSE
20
1_555
covale
1.330
both
B
A
GLU
37
A
C
GLU
19
1_555
A
MSE
38
A
N
MSE
20
1_555
covale
1.327
both
A
MSE
38
A
C
MSE
20
1_555
A
ILE
39
A
N
ILE
21
1_555
covale
1.326
both
A
A
TYR
103
A
C
TYR
85
1_555
A
MSE
104
A
N
MSE
86
1_555
covale
1.332
both
B
A
TYR
103
A
C
TYR
85
1_555
A
MSE
104
A
N
MSE
86
1_555
covale
1.320
both
A
MSE
104
A
C
MSE
86
1_555
A
LYS
105
A
N
LYS
87
1_555
covale
1.332
both
B
GLU
37
B
C
GLU
19
1_555
B
MSE
38
B
N
MSE
20
1_555
covale
1.316
both
B
MSE
38
B
C
MSE
20
1_555
B
ILE
39
B
N
ILE
21
1_555
covale
1.330
both
B
TYR
103
B
C
TYR
85
1_555
B
MSE
104
B
N
MSE
86
1_555
covale
1.333
both
B
MSE
104
B
C
MSE
86
1_555
B
LYS
105
B
N
LYS
87
1_555
MEMBRANE PROTEIN
Blip-like fold, structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, membrane protein
A6L337_BACV8
UNP
1
20
A6L337
AGDVVTRDVNKLPVAAREMIGKHFSQTKVAYIKIEKDLFQTTSYDVKLADGIELEFNSKGEWLEIDCKNKSVPSTFIPQA
ISKYMKANYNGHKTVKIERNRKGYELTLENGLEVDFDQFGGFLKLSD
20
146
3ELG
20
146
A6L337
A
1
2
128
20
146
3ELG
20
146
A6L337
B
1
2
128
1
expression tag
GLY
19
3ELG
A
A6L337
UNP
1
2
expression tag
GLY
19
3ELG
B
A6L337
UNP
1
9
9
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
anti-parallel
A
VAL
23
A
VAL
5
A
THR
25
A
THR
7
A
VAL
48
A
VAL
30
A
LYS
55
A
LYS
37
A
THR
61
A
THR
43
A
LEU
67
A
LEU
49
A
GLU
72
A
GLU
54
A
PHE
75
A
PHE
57
A
TRP
81
A
TRP
63
A
ASP
85
A
ASP
67
A
THR
113
A
THR
95
A
ASN
119
A
ASN
101
A
GLY
122
A
GLY
104
A
LEU
127
A
LEU
109
A
GLU
132
A
GLU
114
A
PHE
135
A
PHE
117
A
PHE
141
A
PHE
123
A
SER
145
A
SER
127
B
VAL
23
B
VAL
5
B
THR
25
B
THR
7
B
VAL
48
B
VAL
30
B
LYS
55
B
LYS
37
B
THR
61
B
THR
43
B
LEU
67
B
LEU
49
B
GLU
72
B
GLU
54
B
PHE
75
B
PHE
57
B
TRP
81
B
TRP
63
B
ASP
85
B
ASP
67
B
THR
113
B
THR
95
B
ASN
119
B
ASN
101
B
GLY
122
B
GLY
104
B
LEU
127
B
LEU
109
B
GLU
132
B
GLU
114
B
PHE
135
B
PHE
117
B
PHE
141
B
PHE
123
B
SER
145
B
SER
127
BINDING SITE FOR RESIDUE CIT B 1
B
CIT
1
Software
10
A
THR
60
A
THR
42
10
1_555
A
ASN
76
A
ASN
58
10
1_555
A
SER
77
A
SER
59
10
1_555
A
HOH
208
D
HOH
10
1_555
A
HOH
211
D
HOH
10
1_555
A
HOH
244
D
HOH
10
1_555
A
HOH
272
D
HOH
10
1_555
B
THR
60
B
THR
42
10
1_555
B
ASN
76
B
ASN
58
10
1_555
B
SER
77
B
SER
59
10
1_555
4
P 1 21 1