0.013329
0.000000
0.000000
0.000000
0.013329
0.000000
0.000000
0.000000
0.007856
0.000000
0.000000
0.000000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.000
90.000
90.000
75.025
75.025
127.290
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
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
O4 S -2
96.063
SULFATE ION
non-polymer
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 outer membrane protein, part of carbohydrate binding complex (NP_809935.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.93 A resolution
10.2210/pdb3g6i/pdb
pdb_00003g6i
100
1
Flat collimating mirror, toroid focusing mirror
CCD
2009-01-17
MARMOSAIC 325 mm CCD
Double crystal
MAD
M
x-ray
1
0.91837
1.0
0.97964
1.0
0.97949
1.0
BL9-2
SSRL
0.91837, 0.97964, 0.97949
SYNCHROTRON
SSRL BEAMLINE BL9-2
23237.840
Putative outer membrane protein, part of carbohydrate binding complex
UNP residues 20-222
1
man
polymer
106.120
DI(HYDROXYETHYL)ETHER
2
syn
non-polymer
96.063
SULFATE ION
1
syn
non-polymer
18.015
water
238
nat
water
no
yes
GAVDLNKENRDPKYVESIVNRSQKIVDKLGLTDAKVAEDVCNVIANRYFELNDIYEIRDAKVKAVKESGLTGDAKNEALK
AAENEKDAALYRSHFAFPASLSLFLNEEQIEAVKDG(MSE)TYGVVKVTYEATLD(MSE)IPSLKEEEKVQIYAWLVEAR
EFA(MSE)DAENSNKKHAAFGKYKGRINNYLAKRGYNLTKEREEWAKRVKARGGTL
GAVDLNKENRDPKYVESIVNRSQKIVDKLGLTDAKVAEDVCNVIANRYFELNDIYEIRDAKVKAVKESGLTGDAKNEALK
AAENEKDAALYRSHFAFPASLSLFLNEEQIEAVKDGMTYGVVKVTYEATLDMIPSLKEEEKVQIYAWLVEAREFAMDAEN
SNKKHAAFGKYKGRINNYLAKRGYNLTKEREEWAKRVKARGGTL
A
393061
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
VPI-5482 / DSM 2079 / NCTC 10582 / E50
sample
29148
BT_1022, NP_809935.1
226186
Bacteroides thetaiotaomicron VPI-5482
562
Escherichia coli
HK100
Plasmid
SpeedET
1
3.85
68.09
VAPOR DIFFUSION, SITTING DROP
8.67
NANODROP, 0.25M Lithium sulfate, 34.0% PEG 4000, 0.1M Tris-HCl pH 8.67, 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
2009-02-17
1
1
2011-07-13
1
2
2017-11-01
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
2009-02-06
REL
REL
PEG
DI(HYDROXYETHYL)ETHER
SO4
SULFATE ION
HOH
water
THE CONSTRUCT (RESIDUES 20-222) WAS EXPRESSED WITH A
PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED
WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY
THE TARGET SEQUENCE.
PEG
1
2
PEG
PEG
1
A
PEG
2
2
PEG
PEG
2
A
SO4
3
3
SO4
SO4
3
A
HOH
4
4
HOH
HOH
4
A
HOH
5
4
HOH
HOH
5
A
HOH
6
4
HOH
HOH
6
A
HOH
7
4
HOH
HOH
7
A
HOH
8
4
HOH
HOH
8
A
HOH
9
4
HOH
HOH
9
A
HOH
10
4
HOH
HOH
10
A
HOH
11
4
HOH
HOH
11
A
HOH
12
4
HOH
HOH
12
A
HOH
13
4
HOH
HOH
13
A
HOH
14
4
HOH
HOH
14
A
HOH
15
4
HOH
HOH
15
A
HOH
16
4
HOH
HOH
16
A
HOH
17
4
HOH
HOH
17
A
HOH
18
4
HOH
HOH
18
A
HOH
223
4
HOH
HOH
223
A
HOH
224
4
HOH
HOH
224
A
HOH
225
4
HOH
HOH
225
A
HOH
226
4
HOH
HOH
226
A
HOH
227
4
HOH
HOH
227
A
HOH
228
4
HOH
HOH
228
A
HOH
229
4
HOH
HOH
229
A
HOH
230
4
HOH
HOH
230
A
HOH
231
4
HOH
HOH
231
A
HOH
232
4
HOH
HOH
232
A
HOH
233
4
HOH
HOH
233
A
HOH
234
4
HOH
HOH
234
A
HOH
235
4
HOH
HOH
235
A
HOH
236
4
HOH
HOH
236
A
HOH
237
4
HOH
HOH
237
A
HOH
238
4
HOH
HOH
238
A
HOH
239
4
HOH
HOH
239
A
HOH
240
4
HOH
HOH
240
A
HOH
241
4
HOH
HOH
241
A
HOH
19
4
HOH
HOH
242
A
HOH
20
4
HOH
HOH
243
A
HOH
21
4
HOH
HOH
244
A
HOH
22
4
HOH
HOH
245
A
HOH
23
4
HOH
HOH
246
A
HOH
24
4
HOH
HOH
247
A
HOH
25
4
HOH
HOH
248
A
HOH
26
4
HOH
HOH
249
A
HOH
27
4
HOH
HOH
250
A
HOH
28
4
HOH
HOH
251
A
HOH
29
4
HOH
HOH
252
A
HOH
30
4
HOH
HOH
253
A
HOH
31
4
HOH
HOH
254
A
HOH
32
4
HOH
HOH
255
A
HOH
33
4
HOH
HOH
256
A
HOH
34
4
HOH
HOH
257
A
HOH
35
4
HOH
HOH
258
A
HOH
36
4
HOH
HOH
259
A
HOH
37
4
HOH
HOH
260
A
HOH
38
4
HOH
HOH
261
A
HOH
39
4
HOH
HOH
262
A
HOH
40
4
HOH
HOH
263
A
HOH
41
4
HOH
HOH
264
A
HOH
42
4
HOH
HOH
265
A
HOH
43
4
HOH
HOH
266
A
HOH
44
4
HOH
HOH
267
A
HOH
45
4
HOH
HOH
268
A
HOH
46
4
HOH
HOH
269
A
HOH
47
4
HOH
HOH
270
A
HOH
48
4
HOH
HOH
271
A
HOH
49
4
HOH
HOH
272
A
HOH
50
4
HOH
HOH
273
A
HOH
51
4
HOH
HOH
274
A
HOH
52
4
HOH
HOH
275
A
HOH
53
4
HOH
HOH
276
A
HOH
54
4
HOH
HOH
277
A
HOH
55
4
HOH
HOH
278
A
HOH
56
4
HOH
HOH
279
A
HOH
57
4
HOH
HOH
280
A
HOH
58
4
HOH
HOH
281
A
HOH
59
4
HOH
HOH
282
A
HOH
60
4
HOH
HOH
283
A
HOH
61
4
HOH
HOH
284
A
HOH
62
4
HOH
HOH
285
A
HOH
63
4
HOH
HOH
286
A
HOH
64
4
HOH
HOH
287
A
HOH
65
4
HOH
HOH
288
A
HOH
66
4
HOH
HOH
289
A
HOH
67
4
HOH
HOH
290
A
HOH
68
4
HOH
HOH
291
A
HOH
69
4
HOH
HOH
292
A
HOH
70
4
HOH
HOH
293
A
HOH
71
4
HOH
HOH
294
A
HOH
72
4
HOH
HOH
295
A
HOH
73
4
HOH
HOH
296
A
HOH
74
4
HOH
HOH
297
A
HOH
75
4
HOH
HOH
298
A
HOH
76
4
HOH
HOH
299
A
HOH
77
4
HOH
HOH
300
A
HOH
78
4
HOH
HOH
301
A
HOH
79
4
HOH
HOH
302
A
HOH
80
4
HOH
HOH
303
A
HOH
81
4
HOH
HOH
304
A
HOH
82
4
HOH
HOH
305
A
HOH
83
4
HOH
HOH
306
A
HOH
84
4
HOH
HOH
307
A
HOH
85
4
HOH
HOH
308
A
HOH
86
4
HOH
HOH
309
A
HOH
87
4
HOH
HOH
310
A
HOH
88
4
HOH
HOH
311
A
HOH
89
4
HOH
HOH
312
A
HOH
90
4
HOH
HOH
313
A
HOH
91
4
HOH
HOH
314
A
HOH
92
4
HOH
HOH
315
A
HOH
93
4
HOH
HOH
316
A
HOH
94
4
HOH
HOH
317
A
HOH
95
4
HOH
HOH
318
A
HOH
96
4
HOH
HOH
319
A
HOH
97
4
HOH
HOH
320
A
HOH
98
4
HOH
HOH
321
A
HOH
99
4
HOH
HOH
322
A
HOH
100
4
HOH
HOH
323
A
HOH
101
4
HOH
HOH
324
A
HOH
102
4
HOH
HOH
325
A
HOH
103
4
HOH
HOH
326
A
HOH
104
4
HOH
HOH
327
A
HOH
105
4
HOH
HOH
328
A
HOH
106
4
HOH
HOH
329
A
HOH
107
4
HOH
HOH
330
A
HOH
108
4
HOH
HOH
331
A
HOH
109
4
HOH
HOH
332
A
HOH
110
4
HOH
HOH
333
A
HOH
111
4
HOH
HOH
334
A
HOH
112
4
HOH
HOH
335
A
HOH
113
4
HOH
HOH
336
A
HOH
114
4
HOH
HOH
337
A
HOH
115
4
HOH
HOH
338
A
HOH
116
4
HOH
HOH
339
A
HOH
117
4
HOH
HOH
340
A
HOH
118
4
HOH
HOH
341
A
HOH
119
4
HOH
HOH
342
A
HOH
120
4
HOH
HOH
343
A
HOH
121
4
HOH
HOH
344
A
HOH
122
4
HOH
HOH
345
A
HOH
123
4
HOH
HOH
346
A
HOH
124
4
HOH
HOH
347
A
HOH
125
4
HOH
HOH
348
A
HOH
126
4
HOH
HOH
349
A
HOH
127
4
HOH
HOH
350
A
HOH
128
4
HOH
HOH
351
A
HOH
129
4
HOH
HOH
352
A
HOH
130
4
HOH
HOH
353
A
HOH
131
4
HOH
HOH
354
A
HOH
132
4
HOH
HOH
355
A
HOH
133
4
HOH
HOH
356
A
HOH
134
4
HOH
HOH
357
A
HOH
135
4
HOH
HOH
358
A
HOH
136
4
HOH
HOH
359
A
HOH
137
4
HOH
HOH
360
A
HOH
138
4
HOH
HOH
361
A
HOH
139
4
HOH
HOH
362
A
HOH
140
4
HOH
HOH
363
A
HOH
141
4
HOH
HOH
364
A
HOH
142
4
HOH
HOH
365
A
HOH
143
4
HOH
HOH
366
A
HOH
144
4
HOH
HOH
367
A
HOH
145
4
HOH
HOH
368
A
HOH
146
4
HOH
HOH
369
A
HOH
147
4
HOH
HOH
370
A
HOH
148
4
HOH
HOH
371
A
HOH
149
4
HOH
HOH
372
A
HOH
150
4
HOH
HOH
373
A
HOH
151
4
HOH
HOH
374
A
HOH
152
4
HOH
HOH
375
A
HOH
153
4
HOH
HOH
376
A
HOH
154
4
HOH
HOH
377
A
HOH
155
4
HOH
HOH
378
A
HOH
156
4
HOH
HOH
379
A
HOH
157
4
HOH
HOH
380
A
HOH
158
4
HOH
HOH
381
A
HOH
159
4
HOH
HOH
382
A
HOH
160
4
HOH
HOH
383
A
HOH
161
4
HOH
HOH
384
A
HOH
162
4
HOH
HOH
385
A
HOH
163
4
HOH
HOH
386
A
HOH
164
4
HOH
HOH
387
A
HOH
165
4
HOH
HOH
388
A
HOH
166
4
HOH
HOH
389
A
HOH
167
4
HOH
HOH
390
A
HOH
168
4
HOH
HOH
391
A
HOH
169
4
HOH
HOH
392
A
HOH
170
4
HOH
HOH
393
A
HOH
171
4
HOH
HOH
394
A
HOH
172
4
HOH
HOH
395
A
HOH
173
4
HOH
HOH
396
A
HOH
174
4
HOH
HOH
397
A
HOH
175
4
HOH
HOH
398
A
HOH
176
4
HOH
HOH
399
A
HOH
177
4
HOH
HOH
400
A
HOH
178
4
HOH
HOH
401
A
HOH
179
4
HOH
HOH
402
A
HOH
180
4
HOH
HOH
403
A
HOH
181
4
HOH
HOH
404
A
HOH
182
4
HOH
HOH
405
A
HOH
183
4
HOH
HOH
406
A
HOH
184
4
HOH
HOH
407
A
HOH
185
4
HOH
HOH
408
A
HOH
186
4
HOH
HOH
409
A
HOH
187
4
HOH
HOH
410
A
HOH
188
4
HOH
HOH
411
A
HOH
189
4
HOH
HOH
412
A
HOH
190
4
HOH
HOH
413
A
HOH
191
4
HOH
HOH
414
A
HOH
192
4
HOH
HOH
415
A
HOH
193
4
HOH
HOH
416
A
HOH
194
4
HOH
HOH
417
A
HOH
195
4
HOH
HOH
418
A
HOH
196
4
HOH
HOH
419
A
HOH
197
4
HOH
HOH
420
A
HOH
198
4
HOH
HOH
421
A
HOH
199
4
HOH
HOH
422
A
HOH
200
4
HOH
HOH
423
A
HOH
201
4
HOH
HOH
424
A
HOH
202
4
HOH
HOH
425
A
HOH
203
4
HOH
HOH
426
A
HOH
204
4
HOH
HOH
427
A
HOH
205
4
HOH
HOH
428
A
HOH
206
4
HOH
HOH
429
A
HOH
207
4
HOH
HOH
430
A
HOH
208
4
HOH
HOH
431
A
HOH
209
4
HOH
HOH
432
A
HOH
210
4
HOH
HOH
433
A
HOH
211
4
HOH
HOH
434
A
HOH
212
4
HOH
HOH
435
A
HOH
213
4
HOH
HOH
436
A
HOH
214
4
HOH
HOH
437
A
HOH
215
4
HOH
HOH
438
A
HOH
216
4
HOH
HOH
439
A
HOH
217
4
HOH
HOH
440
A
HOH
218
4
HOH
HOH
441
A
HOH
219
4
HOH
HOH
442
A
HOH
220
4
HOH
HOH
443
A
HOH
221
4
HOH
HOH
444
A
HOH
222
4
HOH
HOH
445
A
n
1
19
A
ALA
20
n
2
ALA
20
A
VAL
21
n
3
VAL
21
A
ASP
22
n
4
ASP
22
A
LEU
23
n
5
LEU
23
A
ASN
24
n
6
ASN
24
A
LYS
25
n
7
LYS
25
A
GLU
26
n
8
GLU
26
A
ASN
27
n
9
ASN
27
A
ARG
28
n
10
ARG
28
A
ASP
29
n
11
ASP
29
A
PRO
30
n
12
PRO
30
A
LYS
31
n
13
LYS
31
A
TYR
32
n
14
TYR
32
A
VAL
33
n
15
VAL
33
A
GLU
34
n
16
GLU
34
A
SER
35
n
17
SER
35
A
ILE
36
n
18
ILE
36
A
VAL
37
n
19
VAL
37
A
ASN
38
n
20
ASN
38
A
ARG
39
n
21
ARG
39
A
SER
40
n
22
SER
40
A
GLN
41
n
23
GLN
41
A
LYS
42
n
24
LYS
42
A
ILE
43
n
25
ILE
43
A
VAL
44
n
26
VAL
44
A
ASP
45
n
27
ASP
45
A
LYS
46
n
28
LYS
46
A
LEU
47
n
29
LEU
47
A
GLY
48
n
30
GLY
48
A
LEU
49
n
31
LEU
49
A
THR
50
n
32
THR
50
A
ASP
51
n
33
ASP
51
A
ALA
52
n
34
ALA
52
A
LYS
53
n
35
LYS
53
A
VAL
54
n
36
VAL
54
A
ALA
55
n
37
ALA
55
A
GLU
56
n
38
GLU
56
A
ASP
57
n
39
ASP
57
A
VAL
58
n
40
VAL
58
A
CYS
59
n
41
CYS
59
A
ASN
60
n
42
ASN
60
A
VAL
61
n
43
VAL
61
A
ILE
62
n
44
ILE
62
A
ALA
63
n
45
ALA
63
A
ASN
64
n
46
ASN
64
A
ARG
65
n
47
ARG
65
A
TYR
66
n
48
TYR
66
A
PHE
67
n
49
PHE
67
A
GLU
68
n
50
GLU
68
A
LEU
69
n
51
LEU
69
A
ASN
70
n
52
ASN
70
A
ASP
71
n
53
ASP
71
A
ILE
72
n
54
ILE
72
A
TYR
73
n
55
TYR
73
A
GLU
74
n
56
GLU
74
A
ILE
75
n
57
ILE
75
A
ARG
76
n
58
ARG
76
A
ASP
77
n
59
ASP
77
A
ALA
78
n
60
ALA
78
A
LYS
79
n
61
LYS
79
A
VAL
80
n
62
VAL
80
A
LYS
81
n
63
LYS
81
A
ALA
82
n
64
ALA
82
A
VAL
83
n
65
VAL
83
A
LYS
84
n
66
LYS
84
A
GLU
85
n
67
GLU
85
A
SER
86
n
68
SER
86
A
GLY
87
n
69
GLY
87
A
LEU
88
n
70
LEU
88
A
THR
89
n
71
THR
89
A
GLY
90
n
72
GLY
90
A
ASP
91
n
73
ASP
91
A
ALA
92
n
74
ALA
92
A
LYS
93
n
75
LYS
93
A
ASN
94
n
76
ASN
94
A
GLU
95
n
77
GLU
95
A
ALA
96
n
78
ALA
96
A
LEU
97
n
79
LEU
97
A
LYS
98
n
80
LYS
98
A
ALA
99
n
81
ALA
99
A
ALA
100
n
82
ALA
100
A
GLU
101
n
83
GLU
101
A
ASN
102
n
84
ASN
102
A
GLU
103
n
85
GLU
103
A
LYS
104
n
86
LYS
104
A
ASP
105
n
87
ASP
105
A
ALA
106
n
88
ALA
106
A
ALA
107
n
89
ALA
107
A
LEU
108
n
90
LEU
108
A
TYR
109
n
91
TYR
109
A
ARG
110
n
92
ARG
110
A
SER
111
n
93
SER
111
A
HIS
112
n
94
HIS
112
A
PHE
113
n
95
PHE
113
A
ALA
114
n
96
ALA
114
A
PHE
115
n
97
PHE
115
A
PRO
116
n
98
PRO
116
A
ALA
117
n
99
ALA
117
A
SER
118
n
100
SER
118
A
LEU
119
n
101
LEU
119
A
SER
120
n
102
SER
120
A
LEU
121
n
103
LEU
121
A
PHE
122
n
104
PHE
122
A
LEU
123
n
105
LEU
123
A
ASN
124
n
106
ASN
124
A
GLU
125
n
107
GLU
125
A
GLU
126
n
108
GLU
126
A
GLN
127
n
109
GLN
127
A
ILE
128
n
110
ILE
128
A
GLU
129
n
111
GLU
129
A
ALA
130
n
112
ALA
130
A
VAL
131
n
113
VAL
131
A
LYS
132
n
114
LYS
132
A
ASP
133
n
115
ASP
133
A
GLY
134
n
116
GLY
134
A
MSE
135
n
117
MSE
135
A
THR
136
n
118
THR
136
A
TYR
137
n
119
TYR
137
A
GLY
138
n
120
GLY
138
A
VAL
139
n
121
VAL
139
A
VAL
140
n
122
VAL
140
A
LYS
141
n
123
LYS
141
A
VAL
142
n
124
VAL
142
A
THR
143
n
125
THR
143
A
TYR
144
n
126
TYR
144
A
GLU
145
n
127
GLU
145
A
ALA
146
n
128
ALA
146
A
THR
147
n
129
THR
147
A
LEU
148
n
130
LEU
148
A
ASP
149
n
131
ASP
149
A
MSE
150
n
132
MSE
150
A
ILE
151
n
133
ILE
151
A
PRO
152
n
134
PRO
152
A
SER
153
n
135
SER
153
A
LEU
154
n
136
LEU
154
A
LYS
155
n
137
LYS
155
A
GLU
156
n
138
GLU
156
A
GLU
157
n
139
GLU
157
A
GLU
158
n
140
GLU
158
A
LYS
159
n
141
LYS
159
A
VAL
160
n
142
VAL
160
A
GLN
161
n
143
GLN
161
A
ILE
162
n
144
ILE
162
A
TYR
163
n
145
TYR
163
A
ALA
164
n
146
ALA
164
A
TRP
165
n
147
TRP
165
A
LEU
166
n
148
LEU
166
A
VAL
167
n
149
VAL
167
A
GLU
168
n
150
GLU
168
A
ALA
169
n
151
ALA
169
A
ARG
170
n
152
ARG
170
A
GLU
171
n
153
GLU
171
A
PHE
172
n
154
PHE
172
A
ALA
173
n
155
ALA
173
A
MSE
174
n
156
MSE
174
A
ASP
175
n
157
ASP
175
A
ALA
176
n
158
ALA
176
A
GLU
177
n
159
GLU
177
A
ASN
178
n
160
ASN
178
A
SER
179
n
161
SER
179
A
ASN
180
n
162
ASN
180
A
LYS
181
n
163
LYS
181
A
LYS
182
n
164
LYS
182
A
HIS
183
n
165
HIS
183
A
ALA
184
n
166
ALA
184
A
ALA
185
n
167
ALA
185
A
PHE
186
n
168
PHE
186
A
GLY
187
n
169
GLY
187
A
LYS
188
n
170
LYS
188
A
TYR
189
n
171
TYR
189
A
LYS
190
n
172
LYS
190
A
GLY
191
n
173
GLY
191
A
ARG
192
n
174
ARG
192
A
ILE
193
n
175
ILE
193
A
ASN
194
n
176
ASN
194
A
ASN
195
n
177
ASN
195
A
TYR
196
n
178
TYR
196
A
LEU
197
n
179
LEU
197
A
ALA
198
n
180
ALA
198
A
LYS
199
n
181
LYS
199
A
ARG
200
n
182
ARG
200
A
GLY
201
n
183
GLY
201
A
TYR
202
n
184
TYR
202
A
ASN
203
n
185
ASN
203
A
LEU
204
n
186
LEU
204
A
THR
205
n
187
THR
205
A
LYS
206
n
188
LYS
206
A
GLU
207
n
189
GLU
207
A
ARG
208
n
190
ARG
208
A
GLU
209
n
191
GLU
209
A
GLU
210
n
192
GLU
210
A
TRP
211
n
193
TRP
211
A
ALA
212
n
194
ALA
212
A
LYS
213
n
195
LYS
213
A
ARG
214
n
196
ARG
214
A
VAL
215
n
197
VAL
215
A
LYS
216
n
198
LYS
216
A
ALA
217
n
199
ALA
217
A
ARG
218
n
200
ARG
218
A
GLY
219
n
201
GLY
219
A
n
202
220
A
n
203
221
A
n
204
222
A
0.6209
-0.0918
0.4542
0.6469
-0.0659
0.6914
0.0068
-0.0381
-0.0489
-0.0413
0.0162
-0.0355
0.0792
0.0102
-0.0229
0.0268
-0.0013
0.0008
0.0329
0.0070
0.0091
refined
32.5962
16.2370
68.2445
X-RAY DIFFRACTION
A
20
A
219
X-RAY DIFFRACTION
1
software_defined_assembly
PISA
2
dimeric
2000
-18.1
22290
A
MSE
135
SELENOMETHIONINE
A
MSE
117
MET
A
MSE
150
SELENOMETHIONINE
A
MSE
132
MET
A
MSE
174
SELENOMETHIONINE
A
MSE
156
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
0.0000000000
1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
7_556
y,x,-z+1
crystal symmetry operation
0.0000000000
0.0000000000
127.2900000000
1
A
CE
LYS
31
A
CE
LYS
13
1
Y
1
A
NZ
LYS
31
A
NZ
LYS
13
1
Y
1
A
CD
LYS
53
A
CD
LYS
35
1
Y
1
A
CE
LYS
53
A
CE
LYS
35
1
Y
1
A
NZ
LYS
53
A
NZ
LYS
35
1
Y
1
A
CD
GLU
95
A
CD
GLU
77
1
Y
1
A
OE1
GLU
95
A
OE1
GLU
77
1
Y
1
A
OE2
GLU
95
A
OE2
GLU
77
1
Y
1
A
CD
ARG
110
A
CD
ARG
92
1
Y
1
A
NE
ARG
110
A
NE
ARG
92
1
Y
1
A
CZ
ARG
110
A
CZ
ARG
92
1
Y
1
A
NH1
ARG
110
A
NH1
ARG
92
1
Y
1
A
NH2
ARG
110
A
NH2
ARG
92
1
Y
1
A
CD
LYS
199
A
CD
LYS
181
1
Y
1
A
CE
LYS
199
A
CE
LYS
181
1
Y
1
A
NZ
LYS
199
A
NZ
LYS
181
1
Y
1
A
GLY
19
A
GLY
1
1
Y
1
A
GLY
220
A
GLY
202
1
Y
1
A
THR
221
A
THR
203
1
Y
1
A
LEU
222
A
LEU
204
1
Y
1
A
THR
89
A
-130.20
-53.57
81.24
32.801
11.84
0.670
0.000
0.000
0.670
0.000
-1.330
0.951
0.939
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. SULFATE AND PEG FRAGMENTS MODELED ARE PRESENT IN CRYSTALLIZATION CONDITIONS.
0.223
0.197
0.198
1.930
48.970
1409
28048
5.000
99.950
1.00
0.25
5.967
0.076
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
0.00
MAD
0.123
0.118
0.800
0.800
1.200
MAXIMUM LIKELIHOOD WITH PHASES
MASK
1.930
48.970
238
1842
19
0
1585
0.017
0.022
1713
0.002
0.020
1192
1.370
1.969
2317
0.917
3.000
2929
4.627
5.000
225
35.245
25.294
85
14.609
15.000
328
15.810
15.000
10
0.085
0.200
252
0.006
0.020
1921
0.001
0.020
335
1.732
3.000
1039
0.525
3.000
422
2.891
5.000
1673
5.149
8.000
674
7.634
11.000
632
0.418
0.371
1.980
89
1926
2015
20
99.850
34.847
1.93
48.970
3G6I
28120
-3.00
0.119
1
14.99
10.8
100.000
1.556
1.93
2.00
1.5
19786
2766
1
100.00
0.983
2.00
2.08
2.5
19767
2741
1
100.00
0.597
2.08
2.17
4.0
19062
2637
1
100.00
0.418
2.17
2.29
5.6
20970
2904
1
100.00
0.459
2.29
2.43
7.9
25707
2714
1
100.00
0.486
2.43
2.62
11.2
40520
2809
1
100.00
0.296
2.62
2.88
15.9
39793
2785
1
100.00
0.147
2.88
3.30
23.5
39982
2852
1
100.00
0.075
3.30
4.15
34.4
38946
2856
1
100.00
0.050
4.15
48.97
39.5
40165
3073
1
99.70
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
5.5.0053
refinement
P.D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
phasing
George M. Sheldrick
gsheldr@shelx.uni-ac.gwdg.de
Fortran_77
http://shelx.uni-ac.gwdg.de/SHELX/
SHELX
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
Wolfgang Kabsch
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html
XSCALE
package
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 collection
MAR345
CCD
data reduction
XDS
phasing
SHELXD
phasing
autoSHARP
Crystal structure of an outer membrane protein, part of a putative carbohydrate binding complex (bt_1022) from bacteroides thetaiotaomicron vpi-5482 at 1.93 A resolution
1
N
N
2
N
N
2
N
N
3
N
N
4
N
N
A
ASP
29
A
ASP
11
HELX_P
A
GLY
48
A
GLY
30
1
1
20
A
ASP
51
A
ASP
33
HELX_P
A
SER
86
A
SER
68
1
2
36
A
GLY
90
A
GLY
72
HELX_P
A
PHE
113
A
PHE
95
1
3
24
A
PHE
113
A
PHE
95
HELX_P
A
SER
120
A
SER
102
1
4
8
A
ASN
124
A
ASN
106
HELX_P
A
THR
136
A
THR
118
1
5
13
A
GLY
138
A
GLY
120
HELX_P
A
ILE
151
A
ILE
133
1
6
14
A
LYS
155
A
LYS
137
HELX_P
A
MSE
174
A
MSE
156
1
7
20
A
ASN
178
A
ASN
160
HELX_P
A
ARG
200
A
ARG
182
1
8
23
A
ASN
203
A
ASN
185
HELX_P
A
GLY
219
A
GLY
201
1
9
17
covale
1.321
both
A
GLY
134
A
C
GLY
116
1_555
A
MSE
135
A
N
MSE
117
1_555
covale
1.319
both
A
MSE
135
A
C
MSE
117
1_555
A
THR
136
A
N
THR
118
1_555
covale
1.318
both
A
ASP
149
A
C
ASP
131
1_555
A
MSE
150
A
N
MSE
132
1_555
covale
1.330
both
A
MSE
150
A
C
MSE
132
1_555
A
ILE
151
A
N
ILE
133
1_555
covale
1.328
both
A
ALA
173
A
C
ALA
155
1_555
A
MSE
174
A
N
MSE
156
1_555
covale
1.341
both
A
MSE
174
A
C
MSE
156
1_555
A
ASP
175
A
N
ASP
157
1_555
UNKNOWN FUNCTION
Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, unknown function
Q8A8Z5_BACTN
UNP
1
20
Q8A8Z5
AVDLNKENRDPKYVESIVNRSQKIVDKLGLTDAKVAEDVCNVIANRYFELNDIYEIRDAKVKAVKESGLTGDAKNEALKA
AENEKDAALYRSHFAFPASLSLFLNEEQIEAVKDGMTYGVVKVTYEATLDMIPSLKEEEKVQIYAWLVEAREFAMDAENS
NKKHAAFGKYKGRINNYLAKRGYNLTKEREEWAKRVKARGGTL
20
222
3G6I
20
222
Q8A8Z5
A
1
2
204
1
expression tag
GLY
19
3G6I
A
Q8A8Z5
UNP
1
BINDING SITE FOR RESIDUE PEG A 1
A
PEG
1
Software
3
BINDING SITE FOR RESIDUE PEG A 2
A
PEG
2
Software
3
BINDING SITE FOR RESIDUE SO4 A 3
A
SO4
3
Software
6
A
TYR
144
A
TYR
126
3
1_555
A
GLU
156
A
GLU
138
3
1_555
A
VAL
160
A
VAL
142
3
1_555
A
LYS
84
A
LYS
66
3
6_456
A
GLU
156
A
GLU
138
3
1_555
A
GLU
157
A
GLU
139
3
1_555
A
ARG
39
A
ARG
21
6
1_555
A
ASN
178
A
ASN
160
6
1_555
A
SER
179
A
SER
161
6
1_555
A
HOH
284
E
HOH
6
1_555
A
HOH
348
E
HOH
6
1_555
A
HOH
417
E
HOH
6
1_555
96
P 43 21 2