0.010137
0.005852
0.000000
0.000000
0.011705
0.000000
0.000000
0.000000
0.005128
0.00000
0.00000
0.00000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.000
90.000
120.000
98.653
98.653
195.018
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
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
C8 H18 O5
194.226
TETRAETHYLENE GLYCOL
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
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 a putative lipoprotein (ycdA) from Bacillus subtilis subsp. subtilis str. 168 at 2.62 A resolution
10.2210/pdb4r4g/pdb
pdb_00004r4g
100
1
Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
PIXEL
2014-06-26
DECTRIS PILATUS 6M
single crystal Si(111) bent
MAD
M
x-ray
1
0.97971
1.0
0.91837
1.0
0.97926
1.0
BL11-1
SSRL
0.97971,0.91837,0.97926
SYNCHROTRON
SSRL BEAMLINE BL11-1
36286.562
putative lipoprotein YcdA
1
man
polymer
194.226
TETRAETHYLENE GLYCOL
3
syn
non-polymer
18.015
water
33
nat
water
no
yes
GEKKESETEKSSDIAQVKIKDVSYTLPSKYDKSTSDDQLVLKVNVAVKNTGKDPLNVDS(MSE)DFTLYQGDTK(MSE)S
DTDPEDYSEKLQGSTINADKSVEGNLFFVVDKGKQYELNYTPESYGDKKPKSVTFKIDGKDKKILATADKLQDSAKALSA
YVDVLLFGKDNADFEKITGANKNEIVNDFNESAKDGYLSASGLSSTYADSKALDNIVNGIKEGLSKNSSIQAKTTSISKD
EAIVEATVKPVDASSLSDRIEDKVKDYYSKNSSASYEEAVKYALQVYPEEFKKLGPASSEKTVEVK(MSE)KKNDIDQWQ
LD(MSE)DDYRAAELVEAFIKE
GEKKESETEKSSDIAQVKIKDVSYTLPSKYDKSTSDDQLVLKVNVAVKNTGKDPLNVDSMDFTLYQGDTKMSDTDPEDYS
EKLQGSTINADKSVEGNLFFVVDKGKQYELNYTPESYGDKKPKSVTFKIDGKDKKILATADKLQDSAKALSAYVDVLLFG
KDNADFEKITGANKNEIVNDFNESAKDGYLSASGLSSTYADSKALDNIVNGIKEGLSKNSSIQAKTTSISKDEAIVEATV
KPVDASSLSDRIEDKVKDYYSKNSSASYEEAVKYALQVYPEEFKKLGPASSEKTVEVKMKKNDIDQWQLDMDDYRAAELV
EAFIKE
A
JCSG-418973
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
ycdA, BSU02780
224308
Bacillus subtilis subsp. subtilis str. 168
562
Escherichia Coli
PB1
Plasmid
SpeedET
1
3.77
67.42
VAPOR DIFFUSION, SITTING DROP
7.0
50.0% polyethylene glycol 200, 0.1M TRIS pH 7.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
277
Joint Center for Structural Genomics
JCSG
PSI:Biology
software
citation_author
database_2
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Refinement description
Database references
Database references
Derived calculations
1
0
2014-09-17
1
1
2017-11-22
1
2
2018-01-24
1
3
2023-02-01
_citation_author.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_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
2014-08-19
REL
REL
PG4
TETRAETHYLENE GLYCOL
HOH
water
THE CONSTRUCT (30-354) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
PG4
401
2
PG4
PG4
401
A
PG4
402
2
PG4
PG4
402
A
PG4
403
2
PG4
PG4
403
A
HOH
404
3
HOH
HOH
501
A
HOH
405
3
HOH
HOH
502
A
HOH
406
3
HOH
HOH
503
A
HOH
407
3
HOH
HOH
504
A
HOH
408
3
HOH
HOH
505
A
HOH
409
3
HOH
HOH
506
A
HOH
410
3
HOH
HOH
507
A
HOH
411
3
HOH
HOH
508
A
HOH
412
3
HOH
HOH
509
A
HOH
413
3
HOH
HOH
510
A
HOH
414
3
HOH
HOH
511
A
HOH
415
3
HOH
HOH
512
A
HOH
416
3
HOH
HOH
513
A
HOH
417
3
HOH
HOH
514
A
HOH
418
3
HOH
HOH
515
A
HOH
419
3
HOH
HOH
516
A
HOH
420
3
HOH
HOH
517
A
HOH
421
3
HOH
HOH
518
A
HOH
422
3
HOH
HOH
519
A
HOH
423
3
HOH
HOH
520
A
HOH
424
3
HOH
HOH
521
A
HOH
425
3
HOH
HOH
522
A
HOH
426
3
HOH
HOH
523
A
HOH
427
3
HOH
HOH
524
A
HOH
428
3
HOH
HOH
525
A
HOH
429
3
HOH
HOH
526
A
HOH
430
3
HOH
HOH
527
A
HOH
431
3
HOH
HOH
528
A
HOH
432
3
HOH
HOH
529
A
HOH
433
3
HOH
HOH
530
A
HOH
434
3
HOH
HOH
531
A
HOH
435
3
HOH
HOH
532
A
HOH
436
3
HOH
HOH
533
A
n
1
0
A
n
2
30
A
n
3
31
A
n
4
32
A
GLU
33
n
5
GLU
33
A
SER
34
n
6
SER
34
A
GLU
35
n
7
GLU
35
A
THR
36
n
8
THR
36
A
GLU
37
n
9
GLU
37
A
LYS
38
n
10
LYS
38
A
SER
39
n
11
SER
39
A
SER
40
n
12
SER
40
A
ASP
41
n
13
ASP
41
A
ILE
42
n
14
ILE
42
A
ALA
43
n
15
ALA
43
A
GLN
44
n
16
GLN
44
A
VAL
45
n
17
VAL
45
A
LYS
46
n
18
LYS
46
A
ILE
47
n
19
ILE
47
A
LYS
48
n
20
LYS
48
A
ASP
49
n
21
ASP
49
A
VAL
50
n
22
VAL
50
A
SER
51
n
23
SER
51
A
TYR
52
n
24
TYR
52
A
THR
53
n
25
THR
53
A
LEU
54
n
26
LEU
54
A
PRO
55
n
27
PRO
55
A
SER
56
n
28
SER
56
A
LYS
57
n
29
LYS
57
A
TYR
58
n
30
TYR
58
A
ASP
59
n
31
ASP
59
A
LYS
60
n
32
LYS
60
A
SER
61
n
33
SER
61
A
THR
62
n
34
THR
62
A
SER
63
n
35
SER
63
A
ASP
64
n
36
ASP
64
A
ASP
65
n
37
ASP
65
A
GLN
66
n
38
GLN
66
A
LEU
67
n
39
LEU
67
A
VAL
68
n
40
VAL
68
A
LEU
69
n
41
LEU
69
A
LYS
70
n
42
LYS
70
A
VAL
71
n
43
VAL
71
A
ASN
72
n
44
ASN
72
A
VAL
73
n
45
VAL
73
A
ALA
74
n
46
ALA
74
A
VAL
75
n
47
VAL
75
A
LYS
76
n
48
LYS
76
A
ASN
77
n
49
ASN
77
A
THR
78
n
50
THR
78
A
GLY
79
n
51
GLY
79
A
LYS
80
n
52
LYS
80
A
ASP
81
n
53
ASP
81
A
PRO
82
n
54
PRO
82
A
LEU
83
n
55
LEU
83
A
ASN
84
n
56
ASN
84
A
VAL
85
n
57
VAL
85
A
ASP
86
n
58
ASP
86
A
SER
87
n
59
SER
87
A
MSE
88
n
60
MSE
88
A
ASP
89
n
61
ASP
89
A
PHE
90
n
62
PHE
90
A
THR
91
n
63
THR
91
A
LEU
92
n
64
LEU
92
A
TYR
93
n
65
TYR
93
A
GLN
94
n
66
GLN
94
A
GLY
95
n
67
GLY
95
A
ASP
96
n
68
ASP
96
A
THR
97
n
69
THR
97
A
LYS
98
n
70
LYS
98
A
MSE
99
n
71
MSE
99
A
SER
100
n
72
SER
100
A
ASP
101
n
73
ASP
101
A
THR
102
n
74
THR
102
A
ASP
103
n
75
ASP
103
A
PRO
104
n
76
PRO
104
A
GLU
105
n
77
GLU
105
A
ASP
106
n
78
ASP
106
A
TYR
107
n
79
TYR
107
A
SER
108
n
80
SER
108
A
GLU
109
n
81
GLU
109
A
LYS
110
n
82
LYS
110
A
LEU
111
n
83
LEU
111
A
GLN
112
n
84
GLN
112
A
GLY
113
n
85
GLY
113
A
SER
114
n
86
SER
114
A
THR
115
n
87
THR
115
A
ILE
116
n
88
ILE
116
A
ASN
117
n
89
ASN
117
A
ALA
118
n
90
ALA
118
A
ASP
119
n
91
ASP
119
A
LYS
120
n
92
LYS
120
A
SER
121
n
93
SER
121
A
VAL
122
n
94
VAL
122
A
GLU
123
n
95
GLU
123
A
GLY
124
n
96
GLY
124
A
ASN
125
n
97
ASN
125
A
LEU
126
n
98
LEU
126
A
PHE
127
n
99
PHE
127
A
PHE
128
n
100
PHE
128
A
VAL
129
n
101
VAL
129
A
VAL
130
n
102
VAL
130
A
ASP
131
n
103
ASP
131
A
LYS
132
n
104
LYS
132
A
GLY
133
n
105
GLY
133
A
LYS
134
n
106
LYS
134
A
GLN
135
n
107
GLN
135
A
TYR
136
n
108
TYR
136
A
GLU
137
n
109
GLU
137
A
LEU
138
n
110
LEU
138
A
ASN
139
n
111
ASN
139
A
TYR
140
n
112
TYR
140
A
THR
141
n
113
THR
141
A
PRO
142
n
114
PRO
142
A
GLU
143
n
115
GLU
143
A
SER
144
n
116
SER
144
A
TYR
145
n
117
TYR
145
A
GLY
146
n
118
GLY
146
A
ASP
147
n
119
ASP
147
A
LYS
148
n
120
LYS
148
A
LYS
149
n
121
LYS
149
A
PRO
150
n
122
PRO
150
A
LYS
151
n
123
LYS
151
A
SER
152
n
124
SER
152
A
VAL
153
n
125
VAL
153
A
THR
154
n
126
THR
154
A
PHE
155
n
127
PHE
155
A
LYS
156
n
128
LYS
156
A
ILE
157
n
129
ILE
157
A
ASP
158
n
130
ASP
158
A
GLY
159
n
131
GLY
159
A
LYS
160
n
132
LYS
160
A
ASP
161
n
133
ASP
161
A
LYS
162
n
134
LYS
162
A
LYS
163
n
135
LYS
163
A
ILE
164
n
136
ILE
164
A
LEU
165
n
137
LEU
165
A
ALA
166
n
138
ALA
166
A
THR
167
n
139
THR
167
A
ALA
168
n
140
ALA
168
A
ASP
169
n
141
ASP
169
A
LYS
170
n
142
LYS
170
A
LEU
171
n
143
LEU
171
A
GLN
172
n
144
GLN
172
A
ASP
173
n
145
ASP
173
A
SER
174
n
146
SER
174
A
ALA
175
n
147
ALA
175
A
LYS
176
n
148
LYS
176
A
ALA
177
n
149
ALA
177
A
LEU
178
n
150
LEU
178
A
SER
179
n
151
SER
179
A
ALA
180
n
152
ALA
180
A
TYR
181
n
153
TYR
181
A
VAL
182
n
154
VAL
182
A
ASP
183
n
155
ASP
183
A
VAL
184
n
156
VAL
184
A
LEU
185
n
157
LEU
185
A
LEU
186
n
158
LEU
186
A
PHE
187
n
159
PHE
187
A
GLY
188
n
160
GLY
188
A
LYS
189
n
161
LYS
189
A
ASP
190
n
162
ASP
190
A
ASN
191
n
163
ASN
191
A
ALA
192
n
164
ALA
192
A
ASP
193
n
165
ASP
193
A
PHE
194
n
166
PHE
194
A
GLU
195
n
167
GLU
195
A
LYS
196
n
168
LYS
196
A
ILE
197
n
169
ILE
197
A
THR
198
n
170
THR
198
A
GLY
199
n
171
GLY
199
A
ALA
200
n
172
ALA
200
A
ASN
201
n
173
ASN
201
A
LYS
202
n
174
LYS
202
A
ASN
203
n
175
ASN
203
A
GLU
204
n
176
GLU
204
A
ILE
205
n
177
ILE
205
A
VAL
206
n
178
VAL
206
A
ASN
207
n
179
ASN
207
A
ASP
208
n
180
ASP
208
A
PHE
209
n
181
PHE
209
A
ASN
210
n
182
ASN
210
A
GLU
211
n
183
GLU
211
A
SER
212
n
184
SER
212
A
ALA
213
n
185
ALA
213
A
LYS
214
n
186
LYS
214
A
ASP
215
n
187
ASP
215
A
GLY
216
n
188
GLY
216
A
TYR
217
n
189
TYR
217
A
LEU
218
n
190
LEU
218
A
SER
219
n
191
SER
219
A
ALA
220
n
192
ALA
220
A
SER
221
n
193
SER
221
A
GLY
222
n
194
GLY
222
A
LEU
223
n
195
LEU
223
A
SER
224
n
196
SER
224
A
SER
225
n
197
SER
225
A
THR
226
n
198
THR
226
A
TYR
227
n
199
TYR
227
A
ALA
228
n
200
ALA
228
A
ASP
229
n
201
ASP
229
A
SER
230
n
202
SER
230
A
LYS
231
n
203
LYS
231
A
ALA
232
n
204
ALA
232
A
LEU
233
n
205
LEU
233
A
ASP
234
n
206
ASP
234
A
ASN
235
n
207
ASN
235
A
ILE
236
n
208
ILE
236
A
VAL
237
n
209
VAL
237
A
ASN
238
n
210
ASN
238
A
GLY
239
n
211
GLY
239
A
ILE
240
n
212
ILE
240
A
LYS
241
n
213
LYS
241
A
GLU
242
n
214
GLU
242
A
GLY
243
n
215
GLY
243
A
LEU
244
n
216
LEU
244
A
SER
245
n
217
SER
245
A
LYS
246
n
218
LYS
246
A
ASN
247
n
219
ASN
247
A
SER
248
n
220
SER
248
A
SER
249
n
221
SER
249
A
ILE
250
n
222
ILE
250
A
GLN
251
n
223
GLN
251
A
ALA
252
n
224
ALA
252
A
LYS
253
n
225
LYS
253
A
THR
254
n
226
THR
254
A
THR
255
n
227
THR
255
A
SER
256
n
228
SER
256
A
ILE
257
n
229
ILE
257
A
SER
258
n
230
SER
258
A
LYS
259
n
231
LYS
259
A
ASP
260
n
232
ASP
260
A
GLU
261
n
233
GLU
261
A
ALA
262
n
234
ALA
262
A
ILE
263
n
235
ILE
263
A
VAL
264
n
236
VAL
264
A
GLU
265
n
237
GLU
265
A
ALA
266
n
238
ALA
266
A
THR
267
n
239
THR
267
A
VAL
268
n
240
VAL
268
A
LYS
269
n
241
LYS
269
A
PRO
270
n
242
PRO
270
A
VAL
271
n
243
VAL
271
A
ASP
272
n
244
ASP
272
A
ALA
273
n
245
ALA
273
A
SER
274
n
246
SER
274
A
SER
275
n
247
SER
275
A
LEU
276
n
248
LEU
276
A
SER
277
n
249
SER
277
A
ASP
278
n
250
ASP
278
A
ARG
279
n
251
ARG
279
A
ILE
280
n
252
ILE
280
A
GLU
281
n
253
GLU
281
A
ASP
282
n
254
ASP
282
A
LYS
283
n
255
LYS
283
A
VAL
284
n
256
VAL
284
A
LYS
285
n
257
LYS
285
A
ASP
286
n
258
ASP
286
A
TYR
287
n
259
TYR
287
A
TYR
288
n
260
TYR
288
A
SER
289
n
261
SER
289
A
LYS
290
n
262
LYS
290
A
ASN
291
n
263
ASN
291
A
SER
292
n
264
SER
292
A
SER
293
n
265
SER
293
A
ALA
294
n
266
ALA
294
A
SER
295
n
267
SER
295
A
TYR
296
n
268
TYR
296
A
GLU
297
n
269
GLU
297
A
GLU
298
n
270
GLU
298
A
ALA
299
n
271
ALA
299
A
VAL
300
n
272
VAL
300
A
LYS
301
n
273
LYS
301
A
TYR
302
n
274
TYR
302
A
ALA
303
n
275
ALA
303
A
LEU
304
n
276
LEU
304
A
GLN
305
n
277
GLN
305
A
VAL
306
n
278
VAL
306
A
TYR
307
n
279
TYR
307
A
PRO
308
n
280
PRO
308
A
GLU
309
n
281
GLU
309
A
GLU
310
n
282
GLU
310
A
PHE
311
n
283
PHE
311
A
LYS
312
n
284
LYS
312
A
LYS
313
n
285
LYS
313
A
LEU
314
n
286
LEU
314
A
GLY
315
n
287
GLY
315
A
PRO
316
n
288
PRO
316
A
ALA
317
n
289
ALA
317
A
SER
318
n
290
SER
318
A
SER
319
n
291
SER
319
A
GLU
320
n
292
GLU
320
A
LYS
321
n
293
LYS
321
A
THR
322
n
294
THR
322
A
VAL
323
n
295
VAL
323
A
GLU
324
n
296
GLU
324
A
VAL
325
n
297
VAL
325
A
LYS
326
n
298
LYS
326
A
MSE
327
n
299
MSE
327
A
LYS
328
n
300
LYS
328
A
LYS
329
n
301
LYS
329
A
ASN
330
n
302
ASN
330
A
ASP
331
n
303
ASP
331
A
ILE
332
n
304
ILE
332
A
ASP
333
n
305
ASP
333
A
GLN
334
n
306
GLN
334
A
TRP
335
n
307
TRP
335
A
GLN
336
n
308
GLN
336
A
LEU
337
n
309
LEU
337
A
ASP
338
n
310
ASP
338
A
MSE
339
n
311
MSE
339
A
ASP
340
n
312
ASP
340
A
ASP
341
n
313
ASP
341
A
TYR
342
n
314
TYR
342
A
ARG
343
n
315
ARG
343
A
ALA
344
n
316
ALA
344
A
ALA
345
n
317
ALA
345
A
GLU
346
n
318
GLU
346
A
LEU
347
n
319
LEU
347
A
VAL
348
n
320
VAL
348
A
GLU
349
n
321
GLU
349
A
ALA
350
n
322
ALA
350
A
PHE
351
n
323
PHE
351
A
ILE
352
n
324
ILE
352
A
LYS
353
n
325
LYS
353
A
GLU
354
n
326
GLU
354
A
0.6088
-0.0593
2.0175
0.5434
0.7999
8.3155
-0.2117
-0.0877
0.0287
0.1853
0.1074
0.0081
-0.4138
-0.3718
0.1043
-0.1615
0.0897
-0.1061
0.0414
-0.0160
-0.1197
refined
1.5638
39.7534
86.9264
X-RAY DIFFRACTION
A
33
A
354
X-RAY DIFFRACTION
1
{A|33 - 354}
author_and_software_defined_assembly
PISA
1
monomeric
A
MSE
88
SELENOMETHIONINE
A
MSE
60
MET
A
MSE
99
SELENOMETHIONINE
A
MSE
71
MET
A
MSE
327
SELENOMETHIONINE
A
MSE
299
MET
A
MSE
339
SELENOMETHIONINE
A
MSE
311
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
38
A
N
LYS
10
A
O
VAL
45
A
O
VAL
17
A
N
SER
51
A
N
SER
23
A
O
LYS
70
A
O
LYS
42
A
N
LEU
69
A
N
LEU
41
A
O
PHE
128
A
O
PHE
100
A
N
LEU
83
A
N
LEU
55
A
O
ILE
116
A
O
ILE
88
A
O
THR
97
A
O
THR
69
A
N
GLN
94
A
N
GLN
66
A
N
THR
91
A
N
THR
63
A
O
ASN
139
A
O
ASN
111
A
N
LEU
138
A
N
LEU
110
A
O
PHE
155
A
O
PHE
127
A
N
LYS
253
A
N
LYS
225
A
O
GLU
265
A
O
GLU
237
A
N
VAL
268
A
N
VAL
240
A
O
LYS
321
A
O
LYS
293
A
N
LYS
328
A
N
LYS
300
A
O
GLN
336
A
O
GLN
308
A
N
VAL
271
A
N
VAL
243
A
O
LYS
353
A
O
LYS
325
1
A
CG
LYS
80
A
CG
LYS
52
1
Y
1
A
CD
LYS
80
A
CD
LYS
52
1
Y
1
A
CE
LYS
80
A
CE
LYS
52
1
Y
1
A
NZ
LYS
80
A
NZ
LYS
52
1
Y
1
A
CG
TYR
145
A
CG
TYR
117
1
Y
1
A
CD1
TYR
145
A
CD1
TYR
117
1
Y
1
A
CD2
TYR
145
A
CD2
TYR
117
1
Y
1
A
CE1
TYR
145
A
CE1
TYR
117
1
Y
1
A
CE2
TYR
145
A
CE2
TYR
117
1
Y
1
A
CZ
TYR
145
A
CZ
TYR
117
1
Y
1
A
OH
TYR
145
A
OH
TYR
117
1
Y
1
A
OG
SER
224
A
OG
SER
196
1
Y
1
A
OG
SER
225
A
OG
SER
197
1
Y
1
A
CG
TYR
342
A
CG
TYR
314
1
Y
1
A
CD1
TYR
342
A
CD1
TYR
314
1
Y
1
A
CD2
TYR
342
A
CD2
TYR
314
1
Y
1
A
CE1
TYR
342
A
CE1
TYR
314
1
Y
1
A
CE2
TYR
342
A
CE2
TYR
314
1
Y
1
A
CZ
TYR
342
A
CZ
TYR
314
1
Y
1
A
OH
TYR
342
A
OH
TYR
314
1
Y
1
A
GLY
0
A
GLY
1
1
Y
1
A
GLU
30
A
GLU
2
1
Y
1
A
LYS
31
A
LYS
3
1
Y
1
A
LYS
32
A
LYS
4
1
Y
1
A
LYS
80
-100.93
-63.63
1
A
ASN
191
-166.13
93.69
1
A
TYR
227
-53.86
-9.70
1
A
ASP
229
-111.59
71.39
1
A
LYS
259
65.70
-114.23
1
A
LYS
290
-84.49
-75.00
1
A
SER
293
-76.48
37.63
166.830
89.4081
49.680
-13.4645
0.0000
0.0000
-13.4645
0.0000
26.9289
0.9180
0.9075
1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. PEG (PG4) MODELED WERE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
0.2389
0.2135
0.2147
2.6200
49.327
889
17574
5.0600
99.8700
1.000
0.370
RANDOM
1
THROUGHOUT
0.000
MAD
0.506
2.6200
49.327
33
2557
39
0
2485
1282
SINUSOIDAL
2.000
89
HARMONIC
2.000
358
HARMONIC
5.000
2586
HARMONIC
20.000
346
SEMIHARMONIC
5.000
2830
SEMIHARMONIC
4.000
0.010
2586
HARMONIC
2.000
1.210
3479
HARMONIC
2.000
3.080
3.120
0.2875
0.2574
0.2591
2.7800
156
2600
2756
9
5.6600
99.8700
84.781
2.62
49.327
4R4G
17632
-3.000
0.090
1
22.880
99.800
0.906
0.023
2.620
2.710
1.8
21199
1640
1638
2.396
1
99.900
0.888
0.023
2.710
2.820
2.5
20805
1753
1745
1.526
1
99.500
0.959
0.023
2.820
2.950
4.0
23416
1749
1744
0.926
1
99.700
0.985
0.023
2.950
3.100
6.4
22234
1667
1667
0.553
1
100.000
0.992
0.023
3.100
3.300
10.2
23782
1795
1794
0.310
1
99.900
0.997
0.023
3.300
3.550
16.8
21857
1709
1706
0.171
1
99.800
0.999
0.023
3.550
3.910
25.5
21926
1771
1769
0.095
1
99.900
0.999
0.023
3.910
4.470
39.4
23315
1772
1772
0.062
1
100.000
1.000
0.023
4.470
5.610
48.6
21313
1793
1790
0.047
1
99.800
1.000
0.023
5.610
64.8
23313
2007
1992
0.031
1
99.300
model building
D.C. & J.S. Richardson lab
molprobity@kinemage.biochem.duke.edu
http://kinemage.biochem.duke.edu/molprobity/
MolProbity
package
3beta29
data extraction
PDB
deposit@deposit.rcsb.org
June 10, 2010
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.10
phasing
George M. Sheldrick
gsheldr@shelx.uni-ac.gwdg.de
Fortran_77
http://shelx.uni-ac.gwdg.de/SHELX/
SHELX
package
phasing
Eric de La Fortelle
sharp-develop@globalphasing.com
http://www.globalphasing.com/sharp/
SHARP
package
data scaling
Wolfgang Kabsch
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html
XSCALE
package
January 10, 2014 BUILT=20140307
refinement
Gerard Bricogne
buster-develop@GlobalPhasing.com
http://www.globalphasing.com/buster/
BUSTER-TNT
program
2.10.0
data reduction
XDS
phasing
SHELXD
refinement
BUSTER
2.10.0
Crystal structure of a putative lipoprotein (ycdA) from Bacillus subtilis subsp. subtilis str. 168 at 2.62 A resolution
1
N
N
2
N
N
2
N
N
2
N
N
3
N
N
CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
A
ASP
86
A
ASP
58
HELX_P
A
MSE
88
A
MSE
60
5
1
3
A
ASP
106
A
ASP
78
HELX_P
A
LYS
110
A
LYS
82
5
2
5
A
ASP
147
A
ASP
119
HELX_P
A
SER
152
A
SER
124
1
3
6
A
ASP
161
A
ASP
133
HELX_P
A
LYS
170
A
LYS
142
1
4
10
A
GLN
172
A
GLN
144
HELX_P
A
LEU
186
A
LEU
158
1
5
15
A
ALA
192
A
ALA
164
HELX_P
A
GLY
199
A
GLY
171
1
6
8
A
ASN
201
A
ASN
173
HELX_P
A
SER
221
A
SER
193
1
7
21
A
SER
224
A
SER
196
HELX_P
A
ASP
229
A
ASP
201
5
8
6
A
SER
230
A
SER
202
HELX_P
A
SER
248
A
SER
220
1
9
19
A
SER
275
A
SER
247
HELX_P
A
SER
289
A
SER
261
1
10
15
A
SER
295
A
SER
267
HELX_P
A
LYS
312
A
LYS
284
1
11
18
A
ASP
341
A
ASP
313
HELX_P
A
ALA
350
A
ALA
322
1
12
10
covale
1.375
both
A
SER
87
A
C
SER
59
1_555
A
MSE
88
A
N
MSE
60
1_555
covale
1.346
both
A
MSE
88
A
C
MSE
60
1_555
A
ASP
89
A
N
ASP
61
1_555
covale
1.345
both
A
LYS
98
A
C
LYS
70
1_555
A
MSE
99
A
N
MSE
71
1_555
covale
1.329
both
A
MSE
99
A
C
MSE
71
1_555
A
SER
100
A
N
SER
72
1_555
covale
1.335
both
A
LYS
326
A
C
LYS
298
1_555
A
MSE
327
A
N
MSE
299
1_555
covale
1.337
both
A
MSE
327
A
C
MSE
299
1_555
A
LYS
328
A
N
LYS
300
1_555
covale
1.335
both
A
ASP
338
A
C
ASP
310
1_555
A
MSE
339
A
N
MSE
311
1_555
covale
1.343
both
A
MSE
339
A
C
MSE
311
1_555
A
ASP
340
A
N
ASP
312
1_555
STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Two domain protein, N-terminal domain has Ig-like fold, belongs to DUF4352 family (PF11611), C-terminal domain has fold: alpha(2)-beta(2)-alpha(2)-beta-alpha; domains connected by kinked-helix, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, UNKNOWN FUNCTION
YCDA_BACSU
UNP
1
30
O34538
EKKESETEKSSDIAQVKIKDVSYTLPSKYDKSTSDDQLVLKVNVAVKNTGKDPLNVDSMDFTLYQGDTKMSDTDPEDYSE
KLQGSTINADKSVEGNLFFVVDKGKQYELNYTPESYGDKKPKSVTFKIDGKDKKILATADKLQDSAKALSAYVDVLLFGK
DNADFEKITGANKNEIVNDFNESAKDGYLSASGLSSTYADSKALDNIVNGIKEGLSKNSSIQAKTTSISKDEAIVEATVK
PVDASSLSDRIEDKVKDYYSKNSSASYEEAVKYALQVYPEEFKKLGPASSEKTVEVKMKKNDIDQWQLDMDDYRAAELVE
AFIKE
30
354
4R4G
30
354
O34538
A
1
2
326
1
expression tag
GLY
0
4R4G
A
O34538
UNP
1
4
2
4
4
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
A
GLU
37
A
GLU
9
A
SER
39
A
SER
11
A
GLN
44
A
GLN
16
A
THR
53
A
THR
25
A
LEU
67
A
LEU
39
A
LYS
76
A
LYS
48
A
SER
121
A
SER
93
A
VAL
130
A
VAL
102
A
LEU
83
A
LEU
55
A
VAL
85
A
VAL
57
A
SER
114
A
SER
86
A
ILE
116
A
ILE
88
A
THR
97
A
THR
69
A
MSE
99
A
MSE
71
A
PHE
90
A
PHE
62
A
GLN
94
A
GLN
66
A
GLN
135
A
GLN
107
A
TYR
140
A
TYR
112
A
VAL
153
A
VAL
125
A
ASP
158
A
ASP
130
A
SER
249
A
SER
221
A
SER
258
A
SER
230
A
GLU
261
A
GLU
233
A
LYS
269
A
LYS
241
A
LYS
321
A
LYS
293
A
LYS
329
A
LYS
301
A
TRP
335
A
TRP
307
A
GLN
336
A
GLN
308
A
VAL
271
A
VAL
243
A
ASP
272
A
ASP
244
A
ILE
352
A
ILE
324
A
LYS
353
A
LYS
325
BINDING SITE FOR RESIDUE PG4 A 401
A
PG4
401
Software
5
BINDING SITE FOR RESIDUE PG4 A 402
A
PG4
402
Software
4
BINDING SITE FOR RESIDUE PG4 A 403
A
PG4
403
Software
3
A
TYR
93
A
TYR
65
5
11_555
A
GLU
137
A
GLU
109
5
11_555
A
ASN
139
A
ASN
111
5
11_555
A
ASN
139
A
ASN
111
5
1_555
A
LYS
149
A
LYS
121
5
1_555
A
LEU
54
A
LEU
26
4
1_555
A
ASP
64
A
ASP
36
4
1_555
A
LYS
253
A
LYS
225
4
1_555
A
THR
255
A
THR
227
4
1_555
A
ALA
213
A
ALA
185
3
1_555
A
ILE
240
A
ILE
212
3
1_555
A
VAL
348
A
VAL
320
3
1_555
179
P 65 2 2