0.009385
0.000000
0.000000
0.000000
0.009385
0.000000
0.000000
0.000000
0.015368
0.00000
0.00000
0.00000
Dong, C.
Hou, H.
Yang, X.
Dong, Y.
Shen, Y.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
106.549
106.549
65.070
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
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
I -1
126.904
IODIDE ION
non-polymer
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 S
149.211
y
METHIONINE
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
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
S
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
C
N
80
N
C
N
81
N
O
N
82
N
N
N
83
N
O
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
N
N
95
S
C
N
96
N
C
N
97
N
O
N
98
N
C
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
O
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
N
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
Y
128
N
C
Y
129
N
N
Y
130
N
C
Y
131
N
C
Y
132
N
N
N
133
N
O
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
O
N
145
N
H
N
146
N
H
N
147
N
N
N
148
S
C
N
149
N
C
N
150
N
O
N
151
S
C
N
152
N
C
N
153
N
C
N
154
N
C
N
155
N
O
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
I
N
170
N
N
N
171
S
C
N
172
N
C
N
173
N
O
N
174
N
C
N
175
N
C
N
176
N
C
N
177
N
C
N
178
N
O
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
N
N
193
S
C
N
194
N
C
N
195
N
O
N
196
N
C
N
197
N
C
N
198
N
C
N
199
N
C
N
200
N
N
N
201
N
O
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
N
N
218
S
C
N
219
N
C
N
220
N
O
N
221
N
C
N
222
N
C
N
223
N
S
N
224
N
C
N
225
N
O
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
N
N
238
S
C
N
239
N
C
N
240
N
O
N
241
N
C
Y
242
N
C
Y
243
N
C
Y
244
N
C
Y
245
N
C
Y
246
N
C
Y
247
N
C
N
248
N
O
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
N
N
261
S
C
N
262
N
C
N
263
N
O
N
264
N
C
N
265
N
C
N
266
N
C
N
267
N
O
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
N
N
278
S
C
N
279
N
C
N
280
N
O
N
281
N
C
N
282
N
O
N
283
N
O
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
N
N
292
S
C
N
293
N
C
N
294
N
O
N
295
R
C
N
296
N
O
N
297
N
C
N
298
N
O
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
N
N
309
S
C
N
310
N
C
N
311
N
O
N
312
N
C
Y
313
N
C
Y
314
N
C
Y
315
N
C
Y
316
N
N
Y
317
N
C
Y
318
N
C
Y
319
N
C
Y
320
N
C
Y
321
N
C
N
322
N
O
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
N
N
336
S
C
N
337
N
C
N
338
N
O
N
339
N
C
Y
340
N
C
Y
341
N
C
Y
342
N
C
Y
343
N
C
Y
344
N
C
Y
345
N
C
N
346
N
O
N
347
N
O
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
N
N
360
S
C
N
361
N
C
N
362
N
O
N
363
N
C
N
364
N
C
N
365
N
C
N
366
N
O
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
doub
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
doub
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
doub
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
Y
127
N
sing
Y
128
N
doub
Y
129
N
doub
N
130
N
sing
Y
131
N
sing
N
132
N
sing
Y
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
doub
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
doub
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
doub
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
doub
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
Y
235
N
doub
Y
236
N
sing
Y
237
N
sing
N
238
N
sing
Y
239
N
doub
N
240
N
sing
Y
241
N
doub
N
242
N
sing
Y
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
doub
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
doub
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
doub
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
doub
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
Y
304
N
doub
Y
305
N
sing
Y
306
N
sing
N
307
N
sing
Y
308
N
doub
Y
309
N
sing
Y
310
N
sing
N
311
N
sing
Y
312
N
sing
Y
313
N
doub
N
314
N
sing
Y
315
N
doub
N
316
N
sing
Y
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
doub
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
Y
332
N
doub
Y
333
N
sing
Y
334
N
sing
N
335
N
sing
Y
336
N
doub
N
337
N
sing
Y
338
N
doub
N
339
N
sing
Y
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
doub
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
68
95
101
10.1107/S0907444911051031
22281737
Structure of Escherichia coli BamD and its functional implications in outer membrane protein assembly
2012
10.2210/pdb3q5m/pdb
pdb_00003q5m
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2010-07-21
MARMOSAIC 325 mm CCD
GRAPHITE
SINGLE WAVELENGTH
M
x-ray
1
0.9791
1.0
3W1A
BSRF
0.9791
SYNCHROTRON
BSRF BEAMLINE 3W1A
25640.625
UPF0169 lipoprotein yfiO
1
man
polymer
126.904
IODIDE ION
7
syn
non-polymer
18.015
water
21
nat
water
Outer membrane protein assembly complex subunit YfiO
no
no
ASKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPT
HPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSV
AEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT
ASKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPT
HPNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSV
AEYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT
A
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
K12
sample
yfiO
83333
Escherichia coli
562
Escherichia coli
1
3.60
65.85
VAPOR DIFFUSION, SITTING DROP
7.0
0.14M KI, 26%-27% PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
277
chem_comp_atom
chem_comp_bond
database_2
struct_ref_seq_dif
struct_site
repository
Initial release
Database references
Database references
Data collection
Database references
Derived calculations
1
0
2011-12-28
1
1
2012-02-01
1
2
2012-05-02
1
3
2024-03-20
_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
RCSB
Y
PDBJ
2010-12-28
REL
REL
IOD
IODIDE ION
HOH
water
I
14
2
IOD
IOD
224
A
I
15
2
IOD
IOD
225
A
I
1
2
IOD
IOD
226
A
I
2
2
IOD
IOD
227
A
I
3
2
IOD
IOD
228
A
I
5
2
IOD
IOD
229
A
I
9
2
IOD
IOD
230
A
HOH
11
3
HOH
HOH
231
A
HOH
12
3
HOH
HOH
232
A
HOH
17
3
HOH
HOH
233
A
HOH
26
3
HOH
HOH
235
A
HOH
28
3
HOH
HOH
236
A
HOH
29
3
HOH
HOH
237
A
HOH
30
3
HOH
HOH
238
A
HOH
31
3
HOH
HOH
239
A
HOH
32
3
HOH
HOH
240
A
HOH
33
3
HOH
HOH
241
A
HOH
34
3
HOH
HOH
242
A
HOH
35
3
HOH
HOH
243
A
HOH
36
3
HOH
HOH
244
A
HOH
37
3
HOH
HOH
245
A
HOH
38
3
HOH
HOH
246
A
HOH
39
3
HOH
HOH
247
A
HOH
40
3
HOH
HOH
248
A
HOH
41
3
HOH
HOH
249
A
HOH
44
3
HOH
HOH
250
A
HOH
48
3
HOH
HOH
251
A
HOH
49
3
HOH
HOH
252
A
ALA
0
n
1
ALA
0
A
SER
1
n
2
SER
1
A
LYS
2
n
3
LYS
2
A
GLU
3
n
4
GLU
3
A
GLU
4
n
5
GLU
4
A
VAL
5
n
6
VAL
5
A
PRO
6
n
7
PRO
6
A
ASP
7
n
8
ASP
7
A
ASN
8
n
9
ASN
8
A
PRO
9
n
10
PRO
9
A
PRO
10
n
11
PRO
10
A
ASN
11
n
12
ASN
11
A
GLU
12
n
13
GLU
12
A
ILE
13
n
14
ILE
13
A
TYR
14
n
15
TYR
14
A
ALA
15
n
16
ALA
15
A
THR
16
n
17
THR
16
A
ALA
17
n
18
ALA
17
A
GLN
18
n
19
GLN
18
A
GLN
19
n
20
GLN
19
A
LYS
20
n
21
LYS
20
A
LEU
21
n
22
LEU
21
A
GLN
22
n
23
GLN
22
A
ASP
23
n
24
ASP
23
A
GLY
24
n
25
GLY
24
A
ASN
25
n
26
ASN
25
A
TRP
26
n
27
TRP
26
A
ARG
27
n
28
ARG
27
A
GLN
28
n
29
GLN
28
A
ALA
29
n
30
ALA
29
A
ILE
30
n
31
ILE
30
A
THR
31
n
32
THR
31
A
GLN
32
n
33
GLN
32
A
LEU
33
n
34
LEU
33
A
GLU
34
n
35
GLU
34
A
ALA
35
n
36
ALA
35
A
LEU
36
n
37
LEU
36
A
ASP
37
n
38
ASP
37
A
ASN
38
n
39
ASN
38
A
ARG
39
n
40
ARG
39
A
TYR
40
n
41
TYR
40
A
PRO
41
n
42
PRO
41
A
PHE
42
n
43
PHE
42
A
GLY
43
n
44
GLY
43
A
PRO
44
n
45
PRO
44
A
TYR
45
n
46
TYR
45
A
SER
46
n
47
SER
46
A
GLN
47
n
48
GLN
47
A
GLN
48
n
49
GLN
48
A
VAL
49
n
50
VAL
49
A
GLN
50
n
51
GLN
50
A
LEU
51
n
52
LEU
51
A
ASP
52
n
53
ASP
52
A
LEU
53
n
54
LEU
53
A
ILE
54
n
55
ILE
54
A
TYR
55
n
56
TYR
55
A
ALA
56
n
57
ALA
56
A
TYR
57
n
58
TYR
57
A
TYR
58
n
59
TYR
58
A
LYS
59
n
60
LYS
59
A
ASN
60
n
61
ASN
60
A
ALA
61
n
62
ALA
61
A
ASP
62
n
63
ASP
62
A
LEU
63
n
64
LEU
63
A
PRO
64
n
65
PRO
64
A
LEU
65
n
66
LEU
65
A
ALA
66
n
67
ALA
66
A
GLN
67
n
68
GLN
67
A
ALA
68
n
69
ALA
68
A
ALA
69
n
70
ALA
69
A
ILE
70
n
71
ILE
70
A
ASP
71
n
72
ASP
71
A
ARG
72
n
73
ARG
72
A
PHE
73
n
74
PHE
73
A
ILE
74
n
75
ILE
74
A
ARG
75
n
76
ARG
75
A
LEU
76
n
77
LEU
76
A
ASN
77
n
78
ASN
77
A
PRO
78
n
79
PRO
78
A
THR
79
n
80
THR
79
A
HIS
80
n
81
HIS
80
A
PRO
81
n
82
PRO
81
A
ASN
82
n
83
ASN
82
A
ILE
83
n
84
ILE
83
A
ASP
84
n
85
ASP
84
A
TYR
85
n
86
TYR
85
A
VAL
86
n
87
VAL
86
A
MET
87
n
88
MET
87
A
TYR
88
n
89
TYR
88
A
MET
89
n
90
MET
89
A
ARG
90
n
91
ARG
90
A
GLY
91
n
92
GLY
91
A
LEU
92
n
93
LEU
92
A
THR
93
n
94
THR
93
A
ASN
94
n
95
ASN
94
A
MET
95
n
96
MET
95
A
ALA
96
n
97
ALA
96
A
LEU
97
n
98
LEU
97
A
ASP
98
n
99
ASP
98
A
ASP
99
n
100
ASP
99
A
ALA
100
n
101
SER
100
A
n
102
101
A
n
103
102
A
n
104
103
A
n
105
104
A
n
106
105
A
n
107
106
A
n
108
107
A
n
109
108
A
n
110
109
A
n
111
110
A
n
112
111
A
n
113
112
A
ARG
113
n
114
ARG
113
A
ASP
114
n
115
ASP
114
A
PRO
115
n
116
PRO
115
A
GLN
116
n
117
GLN
116
A
HIS
117
n
118
HIS
117
A
ALA
118
n
119
ALA
118
A
ARG
119
n
120
ARG
119
A
ALA
120
n
121
ALA
120
A
ALA
121
n
122
ALA
121
A
PHE
122
n
123
PHE
122
A
SER
123
n
124
SER
123
A
ASP
124
n
125
ASP
124
A
PHE
125
n
126
PHE
125
A
SER
126
n
127
SER
126
A
LYS
127
n
128
LYS
127
A
LEU
128
n
129
LEU
128
A
VAL
129
n
130
VAL
129
A
ARG
130
n
131
ARG
130
A
GLY
131
n
132
GLY
131
A
TYR
132
n
133
TYR
132
A
PRO
133
n
134
PRO
133
A
ASN
134
n
135
ASN
134
A
SER
135
n
136
SER
135
A
GLN
136
n
137
GLN
136
A
TYR
137
n
138
TYR
137
A
THR
138
n
139
THR
138
A
THR
139
n
140
THR
139
A
ASP
140
n
141
ASP
140
A
ALA
141
n
142
ALA
141
A
THR
142
n
143
THR
142
A
LYS
143
n
144
LYS
143
A
ARG
144
n
145
ARG
144
A
LEU
145
n
146
LEU
145
A
VAL
146
n
147
VAL
146
A
PHE
147
n
148
PHE
147
A
LEU
148
n
149
LEU
148
A
LYS
149
n
150
LYS
149
A
ASP
150
n
151
ASP
150
A
ARG
151
n
152
ARG
151
A
LEU
152
n
153
LEU
152
A
ALA
153
n
154
ALA
153
A
LYS
154
n
155
LYS
154
A
TYR
155
n
156
TYR
155
A
GLU
156
n
157
GLU
156
A
TYR
157
n
158
TYR
157
A
SER
158
n
159
SER
158
A
VAL
159
n
160
VAL
159
A
ALA
160
n
161
ALA
160
A
GLU
161
n
162
GLU
161
A
TYR
162
n
163
TYR
162
A
TYR
163
n
164
TYR
163
A
THR
164
n
165
THR
164
A
GLU
165
n
166
GLU
165
A
ARG
166
n
167
ARG
166
A
GLY
167
n
168
GLY
167
A
ALA
168
n
169
ALA
168
A
TRP
169
n
170
TRP
169
A
VAL
170
n
171
VAL
170
A
ALA
171
n
172
ALA
171
A
VAL
172
n
173
VAL
172
A
VAL
173
n
174
VAL
173
A
ASN
174
n
175
ASN
174
A
ARG
175
n
176
ARG
175
A
VAL
176
n
177
VAL
176
A
GLU
177
n
178
GLU
177
A
GLY
178
n
179
GLY
178
A
MET
179
n
180
MET
179
A
LEU
180
n
181
LEU
180
A
ARG
181
n
182
ARG
181
A
ASP
182
n
183
ASP
182
A
TYR
183
n
184
TYR
183
A
PRO
184
n
185
PRO
184
A
ASP
185
n
186
ASP
185
A
THR
186
n
187
THR
186
A
GLN
187
n
188
GLN
187
A
ALA
188
n
189
ALA
188
A
THR
189
n
190
THR
189
A
ARG
190
n
191
ARG
190
A
ASP
191
n
192
ASP
191
A
ALA
192
n
193
ALA
192
A
LEU
193
n
194
LEU
193
A
PRO
194
n
195
PRO
194
A
LEU
195
n
196
LEU
195
A
MET
196
n
197
MET
196
A
GLU
197
n
198
GLU
197
A
ASN
198
n
199
ASN
198
A
ALA
199
n
200
ALA
199
A
TYR
200
n
201
TYR
200
A
ARG
201
n
202
ARG
201
A
GLN
202
n
203
GLN
202
A
MET
203
n
204
MET
203
A
GLN
204
n
205
GLN
204
A
MET
205
n
206
MET
205
A
ASN
206
n
207
ASN
206
A
ALA
207
n
208
ALA
207
A
GLN
208
n
209
GLN
208
A
ALA
209
n
210
ALA
209
A
GLU
210
n
211
GLU
210
A
LYS
211
n
212
LYS
211
A
VAL
212
n
213
VAL
212
A
ALA
213
n
214
ALA
213
A
LYS
214
n
215
LYS
214
A
ILE
215
n
216
ILE
215
A
ILE
216
n
217
ILE
216
A
ALA
217
n
218
ALA
217
A
ALA
218
n
219
ALA
218
A
ASN
219
n
220
ASN
219
A
SER
220
n
221
SER
220
A
SER
221
n
222
SER
221
A
n
223
222
A
n
224
223
A
0.4443
-0.4265
-0.0186
2.5224
-1.4925
2.0321
-0.0235
0.1845
-0.0654
-0.2994
-0.1249
0.2624
0.2468
-0.0469
0.0863
0.1536
-0.0263
-0.0443
0.1951
0.0291
0.2221
refined
37.6650
-0.7724
36.5430
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
all
author_defined_assembly
1
monomeric
software_defined_assembly
PISA
2
dimeric
2460
-2
21160
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
6_556
x,-y,-z+3/2
crystal symmetry operation
0.0000000000
0.0000000000
97.6050000000
1
A
HOH
240
I
HOH
1
A
OG
SER
100
A
OG
SER
101
1
Y
1
A
CG
ASP
185
A
CG
ASP
186
1
Y
1
A
OD1
ASP
185
A
OD1
ASP
186
1
Y
1
A
OD2
ASP
185
A
OD2
ASP
186
1
Y
1
A
ALA
101
A
ALA
102
1
Y
1
A
LEU
102
A
LEU
103
1
Y
1
A
GLN
103
A
GLN
104
1
Y
1
A
GLY
104
A
GLY
105
1
Y
1
A
PHE
105
A
PHE
106
1
Y
1
A
PHE
106
A
PHE
107
1
Y
1
A
GLY
107
A
GLY
108
1
Y
1
A
VAL
108
A
VAL
109
1
Y
1
A
ASP
109
A
ASP
110
1
Y
1
A
ARG
110
A
ARG
111
1
Y
1
A
SER
111
A
SER
112
1
Y
1
A
ASP
112
A
ASP
113
1
Y
1
A
ASN
222
A
ASN
223
1
Y
1
A
THR
223
A
THR
224
1
Y
1
A
LYS
2
-164.59
-14.53
1
A
GLU
3
101.12
25.27
3.3238
0.0000
-0.0000
3.3238
0.0000
-6.6477
0.2613
0.2162
0.2207
2.604
32.602
1165
11964
10307
10.01
97.40
0.44
random
1
THROUGHOUT
2.49
2.0
SAD
0.95
1.20
MLHL
FLAT BULK SOLVENT MODEL
39.060
0.333
2.604
32.602
21
1722
7
0
1694
0.009
1731
1.155
2351
17.310
652
0.074
250
0.006
313
0.3602
0.3282
2.7223
136
1225
94.00
0.3437
0.2813
2.8658
136
1228
94.00
0.3346
0.2665
3.0452
143
1277
96.00
0.3194
0.2423
3.2801
142
1284
97.00
0.2636
0.2193
3.6098
147
1316
99.00
0.2099
0.1721
4.1313
147
1333
99.00
0.1852
0.1628
5.2016
153
1368
100.00
0.2885
0.2350
32.6041
161
1448
100.00
2.6
50
3Q5M
11964
10307
5.0
2.0
0.107
0.133
1
41.38
23.3
86.2
0.624
2.60
2.69
2.8
1155
0.643
1
10.4
99.9
refinement
PHENIX
(phenix.refine: 1.6.4_486)
Crystal structure of Escherichia coli BamD
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
A
PRO
9
A
PRO
10
HELX_P
A
ASP
23
A
ASP
24
1
1
15
A
ASN
25
A
ASN
26
HELX_P
A
TYR
40
A
TYR
41
1
2
16
A
TYR
45
A
TYR
46
HELX_P
A
ASN
60
A
ASN
61
1
3
16
A
ASP
62
A
ASP
63
HELX_P
A
ASN
77
A
ASN
78
1
4
16
A
ASN
82
A
ASN
83
HELX_P
A
ASP
99
A
ASP
100
1
5
18
A
PRO
115
A
PRO
116
HELX_P
A
TYR
132
A
TYR
133
1
6
18
A
TYR
137
A
TYR
138
HELX_P
A
ARG
166
A
ARG
167
1
7
30
A
ALA
168
A
ALA
169
HELX_P
A
TYR
183
A
TYR
184
1
8
16
A
THR
186
A
THR
187
HELX_P
A
MET
203
A
MET
204
1
9
18
A
MET
205
A
MET
206
HELX_P
A
ASN
219
A
ASN
220
1
10
15
PROTEIN BINDING
Lipoprotein, BamD, PROTEIN BINDING
A
ALA
0
A
ALA
1
1
A
SER
1
A
SER
2
-5.52
YFIO_ECOLI
UNP
1
23
P0AC02
SKEEVPDNPPNEIYATAQQKLQDGNWRQAITQLEALDNRYPFGPYSQQVQLDLIYAYYKNADLPLAQAAIDRFIRLNPTH
PNIDYVMYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFSDFSKLVRGYPNSQYTTDATKRLVFLKDRLAKYEYSVA
EYYTERGAWVAVVNRVEGMLRDYPDTQATRDALPLMENAYRQMQMNAQAEKVAKIIAANSSNT
23
245
3Q5M
1
223
P0AC02
A
1
2
224
1
expression tag
ALA
0
3Q5M
A
P0AC02
UNP
1
BINDING SITE FOR RESIDUE IOD A 224
A
IOD
224
Software
1
BINDING SITE FOR RESIDUE IOD A 225
A
IOD
225
Software
1
BINDING SITE FOR RESIDUE IOD A 226
A
IOD
226
Software
3
BINDING SITE FOR RESIDUE IOD A 227
A
IOD
227
Software
3
BINDING SITE FOR RESIDUE IOD A 228
A
IOD
228
Software
1
BINDING SITE FOR RESIDUE IOD A 229
A
IOD
229
Software
1
A
PRO
64
A
PRO
65
1
1_555
A
ARG
130
A
ARG
131
1
6_556
A
ASN
8
A
ASN
9
3
1_555
A
ILE
13
A
ILE
14
3
1_555
A
THR
16
A
THR
17
3
1_555
A
GLU
3
A
GLU
4
3
1_555
A
ASN
38
A
ASN
39
3
1_555
A
ARG
39
A
ARG
40
3
1_555
A
TYR
45
A
TYR
46
1
1_555
A
PRO
44
A
PRO
45
1
1_555
91
P 41 2 2