0.014971
0.000000
0.000000
0.000000
0.014217
0.000000
0.000000
0.000000
0.009606
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
66.796
70.337
104.100
C2 H3 O2 -1
59.044
ACETATE ION
non-polymer
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
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
C6 H14 O2
118.174
(4R)-2-METHYLPENTANE-2,4-DIOL
non-polymer
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 pore-forming toxin (YP_001301288.1) from Bacteroides vulgatus ATCC 8482 at 1.85 A resolution
10.2210/pdb3kog/pdb
pdb_00003kog
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
100
1
Flat mirror (vertical focusing)
CCD
2009-06-10
MARMOSAIC 325 mm CCD
Single crystal Si(111) bent monochromator (horizontal focusing)
MAD
M
x-ray
1
0.85503
1.0
0.97926
1.0
0.97845
1.0
BL11-1
SSRL
0.85503,0.97926,0.97845
SYNCHROTRON
SSRL BEAMLINE BL11-1
27777.172
Putative pore-forming toxin
1
man
polymer
59.044
ACETATE ION
3
syn
non-polymer
92.094
GLYCEROL
2
syn
non-polymer
118.174
(4R)-2-METHYLPENTANE-2,4-DIOL
2
syn
non-polymer
18.015
water
169
nat
water
no
yes
GSCEKENIGIEVTPVNAKFIITPVVIDATTGTDVTQSAEISFSKGNGTYEGTPELASESININAKYKG(MSE)TGSASVT
IPALKAGQFGAKEVTIILSENFFAQEESSNSQIETTKHSGFKNNTSDYWYYITVTYTKKEGSEVIKNDYEGDDSEIKNII
DAYNKGVREDKVTLNDVQVLAHSRFSVFVDY(MSE)KTTSVYQIIEKSPKRDGNPVASFTVDSYNTIVSPKNEQIPGHGH
APSHGHGHGHGDDSNAGGGIIIAD
GSCEKENIGIEVTPVNAKFIITPVVIDATTGTDVTQSAEISFSKGNGTYEGTPELASESININAKYKGMTGSASVTIPAL
KAGQFGAKEVTIILSENFFAQEESSNSQIETTKHSGFKNNTSDYWYYITVTYTKKEGSEVIKNDYEGDDSEIKNIIDAYN
KGVREDKVTLNDVQVLAHSRFSVFVDYMKTTSVYQIIEKSPKRDGNPVASFTVDSYNTIVSPKNEQIPGHGHAPSHGHGH
GHGDDSNAGGGIIIAD
A
393242
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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 8482 / DSM 1447 / NCTC 11154
sample
BVU_4064
435590
Bacteroides vulgatus ATCC 8482
562
Escherichia Coli
HK100
Plasmid
SpeedET
1
2.20
44.11
VAPOR DIFFUSION, SITTING DROP
4.43
31.6000% 2-methyl-2,4-pentanediol, 0.2000M sodium chloride, 0.1M sodium acetate pH 4.43, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
Joint Center for Structural Genomics
JCSG
PSI, Protein Structure Initiative
software
pdbx_struct_special_symmetry
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
2009-12-01
1
1
2011-07-13
1
2
2017-11-01
1
3
2019-07-17
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
2009-11-13
REL
REL
ACT
ACETATE ION
GOL
GLYCEROL
MRD
(4R)-2-METHYLPENTANE-2,4-DIOL
HOH
water
SEQUENCE THIS CONSTRUCT (28-282) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
ACT
1
2
ACT
ACT
1
A
ACT
2
2
ACT
ACT
2
A
ACT
3
2
ACT
ACT
3
A
GOL
4
3
GOL
GOL
4
A
GOL
5
3
GOL
GOL
5
A
MRD
6
4
MRD
MRD
6
A
MRD
7
4
MRD
MRD
7
A
HOH
8
5
HOH
HOH
8
A
HOH
9
5
HOH
HOH
9
A
HOH
10
5
HOH
HOH
10
A
HOH
11
5
HOH
HOH
11
A
HOH
12
5
HOH
HOH
12
A
HOH
13
5
HOH
HOH
13
A
HOH
14
5
HOH
HOH
14
A
HOH
15
5
HOH
HOH
15
A
HOH
16
5
HOH
HOH
16
A
HOH
17
5
HOH
HOH
17
A
HOH
18
5
HOH
HOH
18
A
HOH
19
5
HOH
HOH
19
A
HOH
20
5
HOH
HOH
20
A
HOH
21
5
HOH
HOH
21
A
HOH
22
5
HOH
HOH
22
A
HOH
23
5
HOH
HOH
23
A
HOH
24
5
HOH
HOH
24
A
HOH
25
5
HOH
HOH
25
A
HOH
26
5
HOH
HOH
26
A
HOH
27
5
HOH
HOH
283
A
HOH
28
5
HOH
HOH
284
A
HOH
29
5
HOH
HOH
285
A
HOH
30
5
HOH
HOH
286
A
HOH
31
5
HOH
HOH
287
A
HOH
32
5
HOH
HOH
288
A
HOH
33
5
HOH
HOH
289
A
HOH
34
5
HOH
HOH
290
A
HOH
35
5
HOH
HOH
291
A
HOH
36
5
HOH
HOH
292
A
HOH
37
5
HOH
HOH
293
A
HOH
38
5
HOH
HOH
294
A
HOH
39
5
HOH
HOH
295
A
HOH
40
5
HOH
HOH
296
A
HOH
41
5
HOH
HOH
297
A
HOH
42
5
HOH
HOH
298
A
HOH
43
5
HOH
HOH
299
A
HOH
44
5
HOH
HOH
300
A
HOH
45
5
HOH
HOH
301
A
HOH
46
5
HOH
HOH
302
A
HOH
47
5
HOH
HOH
303
A
HOH
48
5
HOH
HOH
304
A
HOH
49
5
HOH
HOH
305
A
HOH
50
5
HOH
HOH
306
A
HOH
51
5
HOH
HOH
307
A
HOH
52
5
HOH
HOH
308
A
HOH
53
5
HOH
HOH
309
A
HOH
54
5
HOH
HOH
310
A
HOH
55
5
HOH
HOH
311
A
HOH
56
5
HOH
HOH
312
A
HOH
57
5
HOH
HOH
313
A
HOH
58
5
HOH
HOH
314
A
HOH
59
5
HOH
HOH
315
A
HOH
60
5
HOH
HOH
316
A
HOH
61
5
HOH
HOH
317
A
HOH
62
5
HOH
HOH
318
A
HOH
63
5
HOH
HOH
319
A
HOH
64
5
HOH
HOH
320
A
HOH
65
5
HOH
HOH
321
A
HOH
66
5
HOH
HOH
322
A
HOH
67
5
HOH
HOH
323
A
HOH
68
5
HOH
HOH
324
A
HOH
69
5
HOH
HOH
325
A
HOH
70
5
HOH
HOH
326
A
HOH
71
5
HOH
HOH
327
A
HOH
72
5
HOH
HOH
328
A
HOH
73
5
HOH
HOH
329
A
HOH
74
5
HOH
HOH
330
A
HOH
75
5
HOH
HOH
331
A
HOH
76
5
HOH
HOH
332
A
HOH
77
5
HOH
HOH
333
A
HOH
78
5
HOH
HOH
334
A
HOH
79
5
HOH
HOH
335
A
HOH
80
5
HOH
HOH
336
A
HOH
81
5
HOH
HOH
337
A
HOH
82
5
HOH
HOH
338
A
HOH
83
5
HOH
HOH
339
A
HOH
84
5
HOH
HOH
340
A
HOH
85
5
HOH
HOH
341
A
HOH
86
5
HOH
HOH
342
A
HOH
87
5
HOH
HOH
343
A
HOH
88
5
HOH
HOH
344
A
HOH
89
5
HOH
HOH
345
A
HOH
90
5
HOH
HOH
346
A
HOH
91
5
HOH
HOH
347
A
HOH
92
5
HOH
HOH
348
A
HOH
93
5
HOH
HOH
349
A
HOH
94
5
HOH
HOH
350
A
HOH
95
5
HOH
HOH
351
A
HOH
96
5
HOH
HOH
352
A
HOH
97
5
HOH
HOH
353
A
HOH
98
5
HOH
HOH
354
A
HOH
99
5
HOH
HOH
355
A
HOH
100
5
HOH
HOH
356
A
HOH
101
5
HOH
HOH
357
A
HOH
102
5
HOH
HOH
358
A
HOH
103
5
HOH
HOH
359
A
HOH
104
5
HOH
HOH
360
A
HOH
105
5
HOH
HOH
361
A
HOH
106
5
HOH
HOH
362
A
HOH
107
5
HOH
HOH
363
A
HOH
108
5
HOH
HOH
364
A
HOH
109
5
HOH
HOH
365
A
HOH
110
5
HOH
HOH
366
A
HOH
111
5
HOH
HOH
367
A
HOH
112
5
HOH
HOH
368
A
HOH
113
5
HOH
HOH
369
A
HOH
114
5
HOH
HOH
370
A
HOH
115
5
HOH
HOH
371
A
HOH
116
5
HOH
HOH
372
A
HOH
117
5
HOH
HOH
373
A
HOH
118
5
HOH
HOH
374
A
HOH
119
5
HOH
HOH
375
A
HOH
120
5
HOH
HOH
376
A
HOH
121
5
HOH
HOH
377
A
HOH
122
5
HOH
HOH
378
A
HOH
123
5
HOH
HOH
379
A
HOH
124
5
HOH
HOH
380
A
HOH
125
5
HOH
HOH
381
A
HOH
126
5
HOH
HOH
382
A
HOH
127
5
HOH
HOH
383
A
HOH
128
5
HOH
HOH
384
A
HOH
129
5
HOH
HOH
385
A
HOH
130
5
HOH
HOH
386
A
HOH
131
5
HOH
HOH
387
A
HOH
132
5
HOH
HOH
388
A
HOH
133
5
HOH
HOH
389
A
HOH
134
5
HOH
HOH
390
A
HOH
135
5
HOH
HOH
391
A
HOH
136
5
HOH
HOH
392
A
HOH
137
5
HOH
HOH
393
A
HOH
138
5
HOH
HOH
394
A
HOH
139
5
HOH
HOH
395
A
HOH
140
5
HOH
HOH
396
A
HOH
141
5
HOH
HOH
397
A
HOH
142
5
HOH
HOH
398
A
HOH
143
5
HOH
HOH
399
A
HOH
144
5
HOH
HOH
400
A
HOH
145
5
HOH
HOH
401
A
HOH
146
5
HOH
HOH
402
A
HOH
147
5
HOH
HOH
403
A
HOH
148
5
HOH
HOH
404
A
HOH
149
5
HOH
HOH
405
A
HOH
150
5
HOH
HOH
406
A
HOH
151
5
HOH
HOH
407
A
HOH
152
5
HOH
HOH
408
A
HOH
153
5
HOH
HOH
409
A
HOH
154
5
HOH
HOH
410
A
HOH
155
5
HOH
HOH
411
A
HOH
156
5
HOH
HOH
412
A
HOH
157
5
HOH
HOH
413
A
HOH
158
5
HOH
HOH
414
A
HOH
159
5
HOH
HOH
415
A
HOH
160
5
HOH
HOH
416
A
HOH
161
5
HOH
HOH
417
A
HOH
162
5
HOH
HOH
418
A
HOH
163
5
HOH
HOH
419
A
HOH
164
5
HOH
HOH
420
A
HOH
165
5
HOH
HOH
421
A
HOH
166
5
HOH
HOH
422
A
HOH
167
5
HOH
HOH
423
A
HOH
168
5
HOH
HOH
424
A
HOH
169
5
HOH
HOH
425
A
HOH
170
5
HOH
HOH
426
A
HOH
171
5
HOH
HOH
427
A
HOH
172
5
HOH
HOH
428
A
HOH
173
5
HOH
HOH
429
A
HOH
174
5
HOH
HOH
430
A
HOH
175
5
HOH
HOH
431
A
HOH
176
5
HOH
HOH
432
A
n
1
0
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
n
8
34
A
n
9
35
A
n
10
36
A
n
11
37
A
n
12
38
A
THR
39
n
13
THR
39
A
PRO
40
n
14
PRO
40
A
VAL
41
n
15
VAL
41
A
ASN
42
n
16
ASN
42
A
ALA
43
n
17
ALA
43
A
LYS
44
n
18
LYS
44
A
PHE
45
n
19
PHE
45
A
ILE
46
n
20
ILE
46
A
ILE
47
n
21
ILE
47
A
THR
48
n
22
THR
48
A
PRO
49
n
23
PRO
49
A
VAL
50
n
24
VAL
50
A
VAL
51
n
25
VAL
51
A
ILE
52
n
26
ILE
52
A
ASP
53
n
27
ASP
53
A
ALA
54
n
28
ALA
54
A
THR
55
n
29
THR
55
A
THR
56
n
30
THR
56
A
GLY
57
n
31
GLY
57
A
THR
58
n
32
THR
58
A
ASP
59
n
33
ASP
59
A
VAL
60
n
34
VAL
60
A
THR
61
n
35
THR
61
A
GLN
62
n
36
GLN
62
A
SER
63
n
37
SER
63
A
ALA
64
n
38
ALA
64
A
GLU
65
n
39
GLU
65
A
ILE
66
n
40
ILE
66
A
SER
67
n
41
SER
67
A
PHE
68
n
42
PHE
68
A
SER
69
n
43
SER
69
A
LYS
70
n
44
LYS
70
A
GLY
71
n
45
GLY
71
A
ASN
72
n
46
ASN
72
A
GLY
73
n
47
GLY
73
A
THR
74
n
48
THR
74
A
TYR
75
n
49
TYR
75
A
GLU
76
n
50
GLU
76
A
GLY
77
n
51
GLY
77
A
THR
78
n
52
THR
78
A
PRO
79
n
53
PRO
79
A
GLU
80
n
54
GLU
80
A
LEU
81
n
55
LEU
81
A
ALA
82
n
56
ALA
82
A
SER
83
n
57
SER
83
A
GLU
84
n
58
GLU
84
A
SER
85
n
59
SER
85
A
ILE
86
n
60
ILE
86
A
ASN
87
n
61
ASN
87
A
ILE
88
n
62
ILE
88
A
ASN
89
n
63
ASN
89
A
ALA
90
n
64
ALA
90
A
LYS
91
n
65
LYS
91
A
TYR
92
n
66
TYR
92
A
LYS
93
n
67
LYS
93
A
GLY
94
n
68
GLY
94
A
MSE
95
n
69
MSE
95
A
THR
96
n
70
THR
96
A
GLY
97
n
71
GLY
97
A
SER
98
n
72
SER
98
A
ALA
99
n
73
ALA
99
A
SER
100
n
74
SER
100
A
VAL
101
n
75
VAL
101
A
THR
102
n
76
THR
102
A
ILE
103
n
77
ILE
103
A
PRO
104
n
78
PRO
104
A
ALA
105
n
79
ALA
105
A
LEU
106
n
80
LEU
106
A
LYS
107
n
81
LYS
107
A
ALA
108
n
82
ALA
108
A
GLY
109
n
83
GLY
109
A
GLN
110
n
84
GLN
110
A
PHE
111
n
85
PHE
111
A
GLY
112
n
86
GLY
112
A
ALA
113
n
87
ALA
113
A
LYS
114
n
88
LYS
114
A
GLU
115
n
89
GLU
115
A
VAL
116
n
90
VAL
116
A
THR
117
n
91
THR
117
A
ILE
118
n
92
ILE
118
A
ILE
119
n
93
ILE
119
A
LEU
120
n
94
LEU
120
A
SER
121
n
95
SER
121
A
GLU
122
n
96
GLU
122
A
ASN
123
n
97
ASN
123
A
PHE
124
n
98
PHE
124
A
PHE
125
n
99
PHE
125
A
ALA
126
n
100
ALA
126
A
GLN
127
n
101
GLN
127
A
GLU
128
n
102
GLU
128
A
GLU
129
n
103
GLU
129
A
SER
130
n
104
SER
130
A
SER
131
n
105
SER
131
A
ASN
132
n
106
ASN
132
A
SER
133
n
107
SER
133
A
GLN
134
n
108
GLN
134
A
ILE
135
n
109
ILE
135
A
GLU
136
n
110
GLU
136
A
THR
137
n
111
THR
137
A
THR
138
n
112
THR
138
A
LYS
139
n
113
LYS
139
A
HIS
140
n
114
HIS
140
A
SER
141
n
115
SER
141
A
GLY
142
n
116
GLY
142
A
PHE
143
n
117
PHE
143
A
LYS
144
n
118
LYS
144
A
ASN
145
n
119
ASN
145
A
ASN
146
n
120
ASN
146
A
THR
147
n
121
THR
147
A
SER
148
n
122
SER
148
A
ASP
149
n
123
ASP
149
A
TYR
150
n
124
TYR
150
A
TRP
151
n
125
TRP
151
A
TYR
152
n
126
TYR
152
A
TYR
153
n
127
TYR
153
A
ILE
154
n
128
ILE
154
A
THR
155
n
129
THR
155
A
VAL
156
n
130
VAL
156
A
THR
157
n
131
THR
157
A
TYR
158
n
132
TYR
158
A
THR
159
n
133
THR
159
A
LYS
160
n
134
LYS
160
A
LYS
161
n
135
LYS
161
A
GLU
162
n
136
GLU
162
A
GLY
163
n
137
GLY
163
A
SER
164
n
138
SER
164
A
GLU
165
n
139
GLU
165
A
VAL
166
n
140
VAL
166
A
ILE
167
n
141
ILE
167
A
LYS
168
n
142
LYS
168
A
ASN
169
n
143
ASN
169
A
ASP
170
n
144
ASP
170
A
TYR
171
n
145
TYR
171
A
GLU
172
n
146
GLU
172
A
GLY
173
n
147
GLY
173
A
ASP
174
n
148
ASP
174
A
ASP
175
n
149
ASP
175
A
SER
176
n
150
SER
176
A
GLU
177
n
151
GLU
177
A
ILE
178
n
152
ILE
178
A
LYS
179
n
153
LYS
179
A
ASN
180
n
154
ASN
180
A
ILE
181
n
155
ILE
181
A
ILE
182
n
156
ILE
182
A
ASP
183
n
157
ASP
183
A
ALA
184
n
158
ALA
184
A
TYR
185
n
159
TYR
185
A
ASN
186
n
160
ASN
186
A
LYS
187
n
161
LYS
187
A
GLY
188
n
162
GLY
188
A
VAL
189
n
163
VAL
189
A
ARG
190
n
164
ARG
190
A
GLU
191
n
165
GLU
191
A
ASP
192
n
166
ASP
192
A
LYS
193
n
167
LYS
193
A
VAL
194
n
168
VAL
194
A
THR
195
n
169
THR
195
A
LEU
196
n
170
LEU
196
A
ASN
197
n
171
ASN
197
A
ASP
198
n
172
ASP
198
A
VAL
199
n
173
VAL
199
A
GLN
200
n
174
GLN
200
A
VAL
201
n
175
VAL
201
A
LEU
202
n
176
LEU
202
A
ALA
203
n
177
ALA
203
A
HIS
204
n
178
HIS
204
A
SER
205
n
179
SER
205
A
ARG
206
n
180
ARG
206
A
PHE
207
n
181
PHE
207
A
SER
208
n
182
SER
208
A
VAL
209
n
183
VAL
209
A
PHE
210
n
184
PHE
210
A
VAL
211
n
185
VAL
211
A
ASP
212
n
186
ASP
212
A
TYR
213
n
187
TYR
213
A
MSE
214
n
188
MSE
214
A
LYS
215
n
189
LYS
215
A
THR
216
n
190
THR
216
A
THR
217
n
191
THR
217
A
SER
218
n
192
SER
218
A
VAL
219
n
193
VAL
219
A
TYR
220
n
194
TYR
220
A
GLN
221
n
195
GLN
221
A
ILE
222
n
196
ILE
222
A
ILE
223
n
197
ILE
223
A
GLU
224
n
198
GLU
224
A
LYS
225
n
199
LYS
225
A
SER
226
n
200
SER
226
A
PRO
227
n
201
PRO
227
A
n
202
228
A
n
203
229
A
ASP
230
n
204
ASP
230
A
GLY
231
n
205
GLY
231
A
ASN
232
n
206
ASN
232
A
PRO
233
n
207
PRO
233
A
VAL
234
n
208
VAL
234
A
ALA
235
n
209
ALA
235
A
SER
236
n
210
SER
236
A
PHE
237
n
211
PHE
237
A
THR
238
n
212
THR
238
A
VAL
239
n
213
VAL
239
A
ASP
240
n
214
ASP
240
A
SER
241
n
215
SER
241
A
TYR
242
n
216
TYR
242
A
ASN
243
n
217
ASN
243
A
THR
244
n
218
THR
244
A
ILE
245
n
219
ILE
245
A
VAL
246
n
220
VAL
246
A
SER
247
n
221
SER
247
A
PRO
248
n
222
PRO
248
A
LYS
249
n
223
LYS
249
A
ASN
250
n
224
ASN
250
A
GLU
251
n
225
GLU
251
A
GLN
252
n
226
GLN
252
A
ILE
253
n
227
ILE
253
A
PRO
254
n
228
PRO
254
A
GLY
255
n
229
GLY
255
A
HIS
256
n
230
HIS
256
A
GLY
257
n
231
GLY
257
A
HIS
258
n
232
HIS
258
A
ALA
259
n
233
ALA
259
A
PRO
260
n
234
PRO
260
A
SER
261
n
235
SER
261
A
HIS
262
n
236
HIS
262
A
GLY
263
n
237
GLY
263
A
HIS
264
n
238
HIS
264
A
GLY
265
n
239
GLY
265
A
HIS
266
n
240
HIS
266
A
n
241
267
A
n
242
268
A
n
243
269
A
n
244
270
A
n
245
271
A
n
246
272
A
n
247
273
A
n
248
274
A
n
249
275
A
n
250
276
A
n
251
277
A
n
252
278
A
n
253
279
A
n
254
280
A
n
255
281
A
n
256
282
A
1.4965
-0.3392
0.2804
1.2485
0.3460
0.7718
-0.0912
-0.0271
0.0376
-0.0529
0.1747
-0.1794
-0.0804
-0.0569
-0.0835
0.0384
-0.0094
0.0137
0.0656
0.0004
0.0528
refined
29.1910
26.4290
48.5930
X-RAY DIFFRACTION
3.5387
2.3669
3.5712
3.3044
3.4333
4.7673
-0.0092
0.4123
-0.1249
-0.0845
0.2816
-0.2361
-0.1165
0.3624
-0.2725
0.0635
-0.0047
0.0352
0.1039
0.0158
0.0501
refined
26.7700
29.9400
38.4470
X-RAY DIFFRACTION
A
39
A
145
X-RAY DIFFRACTION
1
A
146
A
266
X-RAY DIFFRACTION
2
author_defined_assembly
1
monomeric
A
MSE
95
SELENOMETHIONINE
A
MSE
69
MET
A
MSE
214
SELENOMETHIONINE
A
MSE
188
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
O
TYR
75
A
O
TYR
49
A
N
PHE
45
A
N
PHE
19
A
N
ILE
52
A
N
ILE
26
A
O
LEU
120
A
O
LEU
94
A
N
PHE
111
A
N
PHE
85
A
O
VAL
246
A
O
VAL
220
A
O
SER
241
A
O
SER
215
A
N
THR
216
A
N
THR
190
A
O
SER
205
A
O
SER
179
A
N
ASN
146
A
N
ASN
120
A
N
GLN
127
A
N
GLN
101
A
O
GLN
221
A
O
GLN
195
A
N
THR
216
A
N
THR
190
A
O
SER
241
A
O
SER
215
A
O
TYR
242
A
O
TYR
216
A
N
GLY
163
A
N
GLY
137
A
N
GLU
162
A
N
GLU
136
A
O
ARG
190
A
O
ARG
164
A
N
SER
67
A
N
SER
41
A
O
ASN
89
A
O
ASN
63
A
N
ILE
88
A
N
ILE
62
A
O
ALA
99
A
O
ALA
73
1
A
MRD
7
H
MRD
1
A
CE
LYS
91
A
CE
LYS
65
1
Y
1
A
NZ
LYS
91
A
NZ
LYS
65
1
Y
1
A
CE
LYS
107
A
CE
LYS
81
1
Y
1
A
NZ
LYS
107
A
NZ
LYS
81
1
Y
1
A
CE
LYS
144
A
CE
LYS
118
1
Y
1
A
NZ
LYS
144
A
NZ
LYS
118
1
Y
1
A
NZ
LYS
160
A
NZ
LYS
134
1
Y
1
A
NZ
LYS
193
A
NZ
LYS
167
1
Y
1
A
CG
ASN
197
A
CG
ASN
171
1
Y
1
A
OD1
ASN
197
A
OD1
ASN
171
1
Y
1
A
ND2
ASN
197
A
ND2
ASN
171
1
Y
1
A
GLY
0
A
GLY
1
1
Y
1
A
SER
28
A
SER
2
1
Y
1
A
CYS
29
A
CYS
3
1
Y
1
A
GLU
30
A
GLU
4
1
Y
1
A
LYS
31
A
LYS
5
1
Y
1
A
GLU
32
A
GLU
6
1
Y
1
A
ASN
33
A
ASN
7
1
Y
1
A
ILE
34
A
ILE
8
1
Y
1
A
GLY
35
A
GLY
9
1
Y
1
A
ILE
36
A
ILE
10
1
Y
1
A
GLU
37
A
GLU
11
1
Y
1
A
VAL
38
A
VAL
12
1
Y
1
A
LYS
228
A
LYS
202
1
Y
1
A
ARG
229
A
ARG
203
1
Y
1
A
GLY
267
A
GLY
241
1
Y
1
A
HIS
268
A
HIS
242
1
Y
1
A
GLY
269
A
GLY
243
1
Y
1
A
ASP
270
A
ASP
244
1
Y
1
A
ASP
271
A
ASP
245
1
Y
1
A
SER
272
A
SER
246
1
Y
1
A
ASN
273
A
ASN
247
1
Y
1
A
ALA
274
A
ALA
248
1
Y
1
A
GLY
275
A
GLY
249
1
Y
1
A
GLY
276
A
GLY
250
1
Y
1
A
GLY
277
A
GLY
251
1
Y
1
A
ILE
278
A
ILE
252
1
Y
1
A
ILE
279
A
ILE
253
1
Y
1
A
ILE
280
A
ILE
254
1
Y
1
A
ALA
281
A
ALA
255
1
Y
1
A
ASP
282
A
ASP
256
1
Y
1
A
A
OE1
O
GLU
HOH
65
307
2.14
B
1
A
A
OD2
OE2
ASP
GLU
170
172
2.13
A
1_555
6_665
66.51
18.402
4.15
-0.250
0.000
0.000
-0.070
0.000
0.310
0.956
0.945
1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ACETATE (ACT), GLYCEROL (GOL), AND (4R)-2-METHYL-2,4-PENTANEDIOL (MRD) FROM THE CRYSTALLIZATION/CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 5. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
0.214
0.182
0.184
1.850
29.814
1095
21310
5.100
99.990
1.00
0.25
6.503
0.088
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
0.00
MAD
0.142
0.129
0.800
0.800
1.400
MAXIMUM LIKELIHOOD WITH PHASES
MASK
1.850
29.814
169
1938
40
0
1729
0.018
0.022
1944
0.002
0.020
1260
1.621
1.953
2673
0.930
3.000
3143
6.642
5.000
272
39.549
26.264
91
14.076
15.000
325
17.383
15.000
3
0.102
0.200
303
0.007
0.020
2222
0.001
0.020
360
0.959
1.500
1204
0.277
1.500
484
1.697
2.000
1981
2.690
3.000
740
4.300
4.500
669
0.304
0.271
1.898
73
1468
1541
20
100.000
21.528
1.85
29.814
3KOG
21313
0.091
0.091
1
10.200
4.100
100.000
0.726
1.85
1.90
1.0
6377
1549
0.726
1
4.10
100.00
0.565
1.90
1.95
1.0
6196
1507
0.565
1
4.10
100.00
0.439
1.95
2.01
1.7
6068
1475
0.439
1
4.10
100.00
0.340
2.01
2.07
2.1
5914
1437
0.340
1
4.10
100.00
0.294
2.07
2.14
2.5
5672
1378
0.294
1
4.10
100.00
0.262
2.14
2.21
2.8
5591
1355
0.262
1
4.10
100.00
0.220
2.21
2.29
3.3
5376
1309
0.220
1
4.10
100.00
0.189
2.29
2.39
3.9
5139
1246
0.189
1
4.10
100.00
0.167
2.39
2.49
4.4
4928
1201
0.167
1
4.10
100.00
0.142
2.49
2.62
5.0
4762
1163
0.142
1
4.10
100.00
0.115
2.62
2.76
6.2
4495
1098
0.115
1
4.10
100.00
0.097
2.76
2.93
7.1
4235
1035
0.097
1
4.10
100.00
0.081
2.93
3.13
8.1
4029
987
0.081
1
4.10
100.00
0.067
3.13
3.38
9.5
3777
928
0.067
1
4.10
100.00
0.053
3.38
3.70
11.8
3482
858
0.053
1
4.10
100.00
0.043
3.70
4.14
13.8
3093
763
0.043
1
4.10
100.00
0.043
4.14
4.78
13.7
2762
691
0.043
1
4.00
100.00
0.046
4.78
5.85
12.9
2342
591
0.046
1
4.00
100.00
0.043
5.85
8.27
14.2
1787
467
0.043
1
3.80
100.00
0.039
8.27
29.82
15.3
963
275
0.039
1
3.50
98.00
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
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 Putative pore-forming toxin (YP_001301288.1) from Bacteroides vulgatus ATCC 8482 at 1.85 A resolution
1
N
N
2
N
N
2
N
N
2
N
N
3
N
N
3
N
N
4
N
N
4
N
N
5
N
N
A
VAL
60
A
VAL
34
HELX_P
A
ALA
64
A
ALA
38
5
1
5
A
ASP
175
A
ASP
149
HELX_P
A
TYR
185
A
TYR
159
1
2
11
covale
1.323
both
A
MSE
95
A
C
MSE
69
1_555
A
THR
96
A
N
THR
70
1_555
covale
1.329
both
A
MSE
214
A
C
MSE
188
1_555
A
LYS
215
A
N
LYS
189
1_555
MEMBRANE PROTEIN
Putative pore-forming toxin, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, MEMBRANE PROTEIN
A
THR
78
A
THR
52
1
A
PRO
79
A
PRO
53
9.00
A6L7K2_BACV8
UNP
1
28
A6L7K2
SCEKENIGIEVTPVNAKFIITPVVIDATTGTDVTQSAEISFSKGNGTYEGTPELASESININAKYKGMTGSASVTIPALK
AGQFGAKEVTIILSENFFAQEESSNSQIETTKHSGFKNNTSDYWYYITVTYTKKEGSEVIKNDYEGDDSEIKNIIDAYNK
GVREDKVTLNDVQVLAHSRFSVFVDYMKTTSVYQIIEKSPKRDGNPVASFTVDSYNTIVSPKNEQIPGHGHAPSHGHGHG
HGDDSNAGGGIIIAD
28
282
3KOG
28
282
A6L7K2
A
1
2
256
1
expression tag
GLY
0
3KOG
A
A6L7K2
UNP
1
6
5
3
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
THR
74
A
THR
48
A
GLU
76
A
GLU
50
A
LYS
44
A
LYS
18
A
ASP
53
A
ASP
27
A
PHE
111
A
PHE
85
A
LEU
120
A
LEU
94
A
PRO
233
A
PRO
207
A
GLU
251
A
GLU
225
A
SER
205
A
SER
179
A
GLU
224
A
GLU
198
A
LYS
144
A
LYS
118
A
ASN
146
A
ASN
120
A
PHE
124
A
PHE
98
A
HIS
140
A
HIS
114
A
SER
205
A
SER
179
A
GLU
224
A
GLU
198
A
PRO
233
A
PRO
207
A
GLU
251
A
GLU
225
A
TYR
152
A
TYR
126
A
ASN
169
A
ASN
143
A
GLY
188
A
GLY
162
A
VAL
201
A
VAL
175
A
GLU
65
A
GLU
39
A
PHE
68
A
PHE
42
A
GLU
84
A
GLU
58
A
TYR
92
A
TYR
66
A
MSE
95
A
MSE
69
A
ILE
103
A
ILE
77
BINDING SITE FOR RESIDUE ACT A 1
A
ACT
1
Software
2
BINDING SITE FOR RESIDUE ACT A 2
A
ACT
2
Software
1
BINDING SITE FOR RESIDUE GOL A 4
A
GOL
4
Software
8
BINDING SITE FOR RESIDUE GOL A 5
A
GOL
5
Software
7
BINDING SITE FOR RESIDUE MRD A 6
A
MRD
6
Software
3
BINDING SITE FOR RESIDUE MRD A 7
A
MRD
7
Software
5
A
HOH
390
I
HOH
2
1_555
A
HOH
391
I
HOH
2
1_555
A
SER
130
A
SER
104
1
1_555
A
HOH
13
I
HOH
8
1_555
A
GLU
115
A
GLU
89
8
1_555
A
VAL
116
A
VAL
90
8
1_555
A
THR
117
A
THR
91
8
1_555
A
SER
164
A
SER
138
8
1_555
A
TYR
185
A
TYR
159
8
1_555
A
HOH
311
I
HOH
8
1_555
A
HOH
410
I
HOH
8
1_555
A
HOH
25
I
HOH
7
1_555
A
ASP
59
A
ASP
33
7
1_555
A
VAL
60
A
VAL
34
7
1_555
A
THR
61
A
THR
35
7
1_555
A
GLN
62
A
GLN
36
7
1_555
A
HOH
319
I
HOH
7
6_655
A
HOH
328
I
HOH
7
1_555
A
GLN
110
A
GLN
84
3
1_555
A
ASP
212
A
ASP
186
3
1_555
A
HOH
305
I
HOH
3
1_555
A
SER
83
A
SER
57
5
1_555
A
SER
83
A
SER
57
5
7_556
A
SER
85
A
SER
59
5
7_556
A
SER
85
A
SER
59
5
1_555
A
THR
102
A
THR
76
5
1_555
24
I 21 21 21