0.010414
0.000000
0.000000
-0.000000
0.010414
0.000000
0.000000
-0.000000
0.010414
0.000000
0.000000
0.000000
Seattle Structural Genomics Center for Infectious Disease (SSGCID)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
24
90.000
90.000
90.000
96.020
96.020
96.020
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
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 S
149.211
y
METHIONINE
L-peptide linking
Na 1
22.990
SODIUM ION
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
N
1
N
C
N
2
N
O
N
3
N
O
N
4
N
C
N
5
N
H
N
6
N
H
N
7
N
H
N
8
N
N
N
9
S
C
N
10
N
C
N
11
N
O
N
12
N
C
N
13
N
O
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
N
N
22
S
C
N
23
N
C
N
24
N
O
N
25
N
C
N
26
N
C
N
27
N
C
N
28
N
N
N
29
N
C
N
30
N
N
N
31
N
N
N
32
N
O
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
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
N
N
49
S
C
N
50
N
C
N
51
N
O
N
52
N
C
N
53
N
C
N
54
N
O
N
55
N
N
N
56
N
O
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
N
N
66
S
C
N
67
N
C
N
68
N
O
N
69
N
C
N
70
N
C
N
71
N
O
N
72
N
O
N
73
N
O
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
N
N
82
S
C
N
83
N
C
N
84
N
O
N
85
N
C
N
86
N
C
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
O
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
N
N
102
S
C
N
103
N
C
N
104
N
O
N
105
N
C
N
106
N
C
N
107
N
C
N
108
N
O
N
109
N
O
N
110
N
O
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
N
N
121
N
C
N
122
N
C
N
123
N
O
N
124
N
O
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
N
N
131
S
C
N
132
N
C
N
133
N
O
N
134
N
C
Y
135
N
C
Y
136
N
N
Y
137
N
C
Y
138
N
C
Y
139
N
N
N
140
N
O
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
O
N
152
N
H
N
153
N
H
N
154
N
N
N
155
S
C
N
156
N
C
N
157
N
O
N
158
S
C
N
159
N
C
N
160
N
C
N
161
N
C
N
162
N
O
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
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
N
N
177
S
C
N
178
N
C
N
179
N
O
N
180
N
C
N
181
N
C
N
182
N
C
N
183
N
C
N
184
N
O
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
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
N
N
199
S
C
N
200
N
C
N
201
N
O
N
202
N
C
N
203
N
C
N
204
N
C
N
205
N
C
N
206
N
N
N
207
N
O
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
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
N
N
224
S
C
N
225
N
C
N
226
N
O
N
227
N
C
N
228
N
C
N
229
N
S
N
230
N
C
N
231
N
O
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
NA
N
244
N
N
N
245
S
C
N
246
N
C
N
247
N
O
N
248
N
C
Y
249
N
C
Y
250
N
C
Y
251
N
C
Y
252
N
C
Y
253
N
C
Y
254
N
C
N
255
N
O
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
N
N
268
S
C
N
269
N
C
N
270
N
O
N
271
N
C
N
272
N
C
N
273
N
C
N
274
N
O
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
N
N
285
S
C
N
286
N
C
N
287
N
O
N
288
N
C
N
289
N
O
N
290
N
O
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
S
N
299
N
O
N
300
N
O
N
301
N
O
N
302
N
O
N
303
N
N
N
304
S
C
N
305
N
C
N
306
N
O
N
307
R
C
N
308
N
O
N
309
N
C
N
310
N
O
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
N
N
321
S
C
N
322
N
C
N
323
N
O
N
324
N
C
Y
325
N
C
Y
326
N
C
Y
327
N
C
Y
328
N
N
Y
329
N
C
Y
330
N
C
Y
331
N
C
Y
332
N
C
Y
333
N
C
N
334
N
O
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
N
N
348
S
C
N
349
N
C
N
350
N
O
N
351
N
C
Y
352
N
C
Y
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
C
N
358
N
O
N
359
N
O
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
N
N
372
S
C
N
373
N
C
N
374
N
O
N
375
N
C
N
376
N
C
N
377
N
C
N
378
N
O
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
1
N
doub
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
doub
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
doub
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
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
doub
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
doub
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
doub
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
doub
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
doub
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
doub
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
doub
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
doub
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
doub
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
doub
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
Y
133
N
sing
Y
134
N
doub
Y
135
N
doub
N
136
N
sing
Y
137
N
sing
N
138
N
sing
Y
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
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
doub
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
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
doub
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
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
doub
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
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
doub
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
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
doub
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
Y
241
N
doub
Y
242
N
sing
Y
243
N
sing
N
244
N
sing
Y
245
N
doub
N
246
N
sing
Y
247
N
doub
N
248
N
sing
Y
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
doub
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
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
doub
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
doub
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
doub
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
doub
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
Y
314
N
doub
Y
315
N
sing
Y
316
N
sing
N
317
N
sing
Y
318
N
doub
Y
319
N
sing
Y
320
N
sing
N
321
N
sing
Y
322
N
sing
Y
323
N
doub
N
324
N
sing
Y
325
N
doub
N
326
N
sing
Y
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
doub
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
Y
342
N
doub
Y
343
N
sing
Y
344
N
sing
N
345
N
sing
Y
346
N
doub
N
347
N
sing
Y
348
N
doub
N
349
N
sing
Y
350
N
sing
N
351
N
sing
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
doub
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
To be Published
0353
The structure of CyaY from Burkholderia cenocepacia
10.2210/pdb4jpd/pdb
pdb_00004jpd
1
CCD
2012-10-18
ADSC QUANTUM 315r
SINGLE WAVELENGTH
M
x-ray
1
0.97
1.0
5.0.1
ALS
0.97
SYNCHROTRON
ALS BEAMLINE 5.0.1
12236.501
Protein CyaY
1
man
polymer
59.044
ACETATE ION
2
syn
non-polymer
22.990
SODIUM ION
1
syn
non-polymer
96.063
SULFATE ION
1
syn
non-polymer
18.015
water
115
nat
water
no
no
GPGSMSDTEYLARAEAVLAAVERTVDVANDGDHDIDLERNGSVLTLTFENGSKIIVNLQPPMKEVWIAAKAGGFHYRFID
GEWRDTRTGTEFFSALTDYATQQAGLPITFSA
GPGSMSDTEYLARAEAVLAAVERTVDVANDGDHDIDLERNGSVLTLTFENGSKIIVNLQPPMKEVWIAAKAGGFHYRFID
GEWRDTRTGTEFFSALTDYATQQAGLPITFSA
A
SSGCID-BuceA.18084.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
J2315 / LMG 16656
sample
cyaY, BceJ2315_02750, BCAL0273
216591
Burkholderia cenocepacia
562
Escherichia coli
1
3.01
59.20
VAPOR DIFFUSION, SITTING DROP
4.5
50% PEG400, 200mM LiSO4, 100mM Na acetate, 9.46mg/ml BuceA.18084.a.PW33863, direct cryoprotection, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
298
Seattle Structural Genomics Center for Infectious Disease
SSGCID
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
struct_site
repository
Initial release
Data collection
Database references
Derived calculations
Refinement description
1
0
2013-03-27
1
1
2023-09-20
_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
Y
RCSB
Y
RCSB
2013-03-19
REL
REL
ACT
ACETATE ION
NA
SODIUM ION
SO4
SULFATE ION
HOH
water
1EW4
PDB entry 1EW4
PDB
experimental model
ACT
1
2
ACT
ACT
201
A
ACT
2
2
ACT
ACT
202
A
NA
1
3
NA
NA
203
A
SO4
1
4
SO4
SO4
204
A
HOH
2
5
HOH
HOH
301
A
HOH
3
5
HOH
HOH
302
A
HOH
4
5
HOH
HOH
303
A
HOH
5
5
HOH
HOH
304
A
HOH
6
5
HOH
HOH
305
A
HOH
7
5
HOH
HOH
306
A
HOH
8
5
HOH
HOH
307
A
HOH
9
5
HOH
HOH
308
A
HOH
10
5
HOH
HOH
309
A
HOH
11
5
HOH
HOH
310
A
HOH
14
5
HOH
HOH
311
A
HOH
15
5
HOH
HOH
312
A
HOH
16
5
HOH
HOH
313
A
HOH
17
5
HOH
HOH
314
A
HOH
18
5
HOH
HOH
315
A
HOH
19
5
HOH
HOH
316
A
HOH
20
5
HOH
HOH
317
A
HOH
21
5
HOH
HOH
318
A
HOH
23
5
HOH
HOH
319
A
HOH
24
5
HOH
HOH
320
A
HOH
25
5
HOH
HOH
321
A
HOH
26
5
HOH
HOH
322
A
HOH
27
5
HOH
HOH
323
A
HOH
29
5
HOH
HOH
324
A
HOH
30
5
HOH
HOH
325
A
HOH
31
5
HOH
HOH
326
A
HOH
32
5
HOH
HOH
327
A
HOH
33
5
HOH
HOH
328
A
HOH
34
5
HOH
HOH
329
A
HOH
36
5
HOH
HOH
330
A
HOH
37
5
HOH
HOH
331
A
HOH
39
5
HOH
HOH
332
A
HOH
40
5
HOH
HOH
333
A
HOH
41
5
HOH
HOH
334
A
HOH
42
5
HOH
HOH
335
A
HOH
43
5
HOH
HOH
336
A
HOH
44
5
HOH
HOH
337
A
HOH
46
5
HOH
HOH
338
A
HOH
47
5
HOH
HOH
339
A
HOH
48
5
HOH
HOH
340
A
HOH
49
5
HOH
HOH
341
A
HOH
50
5
HOH
HOH
342
A
HOH
51
5
HOH
HOH
343
A
HOH
53
5
HOH
HOH
344
A
HOH
54
5
HOH
HOH
345
A
HOH
55
5
HOH
HOH
346
A
HOH
56
5
HOH
HOH
347
A
HOH
57
5
HOH
HOH
348
A
HOH
58
5
HOH
HOH
349
A
HOH
59
5
HOH
HOH
350
A
HOH
60
5
HOH
HOH
351
A
HOH
61
5
HOH
HOH
352
A
HOH
62
5
HOH
HOH
353
A
HOH
63
5
HOH
HOH
354
A
HOH
64
5
HOH
HOH
355
A
HOH
65
5
HOH
HOH
356
A
HOH
66
5
HOH
HOH
357
A
HOH
67
5
HOH
HOH
358
A
HOH
69
5
HOH
HOH
359
A
HOH
71
5
HOH
HOH
360
A
HOH
72
5
HOH
HOH
361
A
HOH
73
5
HOH
HOH
362
A
HOH
75
5
HOH
HOH
363
A
HOH
76
5
HOH
HOH
364
A
HOH
77
5
HOH
HOH
365
A
HOH
79
5
HOH
HOH
366
A
HOH
80
5
HOH
HOH
367
A
HOH
82
5
HOH
HOH
368
A
HOH
83
5
HOH
HOH
369
A
HOH
84
5
HOH
HOH
370
A
HOH
85
5
HOH
HOH
371
A
HOH
86
5
HOH
HOH
372
A
HOH
88
5
HOH
HOH
373
A
HOH
89
5
HOH
HOH
374
A
HOH
90
5
HOH
HOH
375
A
HOH
92
5
HOH
HOH
376
A
HOH
94
5
HOH
HOH
377
A
HOH
95
5
HOH
HOH
378
A
HOH
96
5
HOH
HOH
379
A
HOH
97
5
HOH
HOH
380
A
HOH
99
5
HOH
HOH
381
A
HOH
100
5
HOH
HOH
382
A
HOH
101
5
HOH
HOH
383
A
HOH
102
5
HOH
HOH
384
A
HOH
103
5
HOH
HOH
385
A
HOH
104
5
HOH
HOH
386
A
HOH
105
5
HOH
HOH
387
A
HOH
106
5
HOH
HOH
388
A
HOH
107
5
HOH
HOH
389
A
HOH
109
5
HOH
HOH
390
A
HOH
110
5
HOH
HOH
391
A
HOH
112
5
HOH
HOH
392
A
HOH
114
5
HOH
HOH
393
A
HOH
116
5
HOH
HOH
394
A
HOH
117
5
HOH
HOH
395
A
HOH
118
5
HOH
HOH
396
A
HOH
119
5
HOH
HOH
397
A
HOH
122
5
HOH
HOH
398
A
HOH
123
5
HOH
HOH
399
A
HOH
125
5
HOH
HOH
400
A
HOH
126
5
HOH
HOH
401
A
HOH
127
5
HOH
HOH
402
A
HOH
128
5
HOH
HOH
403
A
HOH
129
5
HOH
HOH
404
A
HOH
130
5
HOH
HOH
405
A
HOH
131
5
HOH
HOH
406
A
HOH
132
5
HOH
HOH
407
A
HOH
133
5
HOH
HOH
408
A
HOH
134
5
HOH
HOH
409
A
HOH
135
5
HOH
HOH
410
A
HOH
136
5
HOH
HOH
411
A
HOH
137
5
HOH
HOH
412
A
HOH
138
5
HOH
HOH
413
A
HOH
139
5
HOH
HOH
414
A
HOH
140
5
HOH
HOH
415
A
1.950
1.950
48.010
48.010
Phaser MODE: MR_AUTO
n
1
-3
A
n
2
-2
A
n
3
-1
A
SER
0
n
4
SER
0
A
MET
1
n
5
MET
1
A
SER
2
n
6
SER
2
A
ASP
3
n
7
ASP
3
A
THR
4
n
8
THR
4
A
GLU
5
n
9
GLU
5
A
TYR
6
n
10
TYR
6
A
LEU
7
n
11
LEU
7
A
ALA
8
n
12
ALA
8
A
ARG
9
n
13
ARG
9
A
ALA
10
n
14
ALA
10
A
GLU
11
n
15
GLU
11
A
ALA
12
n
16
ALA
12
A
VAL
13
n
17
VAL
13
A
LEU
14
n
18
LEU
14
A
ALA
15
n
19
ALA
15
A
ALA
16
n
20
ALA
16
A
VAL
17
n
21
VAL
17
A
GLU
18
n
22
GLU
18
A
ARG
19
n
23
ARG
19
A
THR
20
n
24
THR
20
A
VAL
21
n
25
VAL
21
A
ASP
22
n
26
ASP
22
A
VAL
23
n
27
VAL
23
A
ALA
24
n
28
ALA
24
A
ASN
25
n
29
ASN
25
A
ASP
26
n
30
ASP
26
A
GLY
27
n
31
GLY
27
A
ASP
28
n
32
ASP
28
A
HIS
29
n
33
HIS
29
A
ASP
30
n
34
ASP
30
A
ILE
31
n
35
ILE
31
A
ASP
32
n
36
ASP
32
A
LEU
33
n
37
LEU
33
A
GLU
34
n
38
GLU
34
A
ARG
35
n
39
ARG
35
A
ASN
36
n
40
ASN
36
A
GLY
37
n
41
GLY
37
A
SER
38
n
42
SER
38
A
VAL
39
n
43
VAL
39
A
LEU
40
n
44
LEU
40
A
THR
41
n
45
THR
41
A
LEU
42
n
46
LEU
42
A
THR
43
n
47
THR
43
A
PHE
44
n
48
PHE
44
A
GLU
45
n
49
GLU
45
A
ASN
46
n
50
ASN
46
A
GLY
47
n
51
GLY
47
A
SER
48
n
52
SER
48
A
LYS
49
n
53
LYS
49
A
ILE
50
n
54
ILE
50
A
ILE
51
n
55
ILE
51
A
VAL
52
n
56
VAL
52
A
ASN
53
n
57
ASN
53
A
LEU
54
n
58
LEU
54
A
GLN
55
n
59
GLN
55
A
PRO
56
n
60
PRO
56
A
PRO
57
n
61
PRO
57
A
MET
58
n
62
MET
58
A
LYS
59
n
63
LYS
59
A
GLU
60
n
64
GLU
60
A
VAL
61
n
65
VAL
61
A
TRP
62
n
66
TRP
62
A
ILE
63
n
67
ILE
63
A
ALA
64
n
68
ALA
64
A
ALA
65
n
69
ALA
65
A
LYS
66
n
70
LYS
66
A
ALA
67
n
71
ALA
67
A
GLY
68
n
72
GLY
68
A
GLY
69
n
73
GLY
69
A
PHE
70
n
74
PHE
70
A
HIS
71
n
75
HIS
71
A
TYR
72
n
76
TYR
72
A
ARG
73
n
77
ARG
73
A
PHE
74
n
78
PHE
74
A
ILE
75
n
79
ILE
75
A
ASP
76
n
80
ASP
76
A
GLY
77
n
81
GLY
77
A
GLU
78
n
82
GLU
78
A
TRP
79
n
83
TRP
79
A
ARG
80
n
84
ARG
80
A
ASP
81
n
85
ASP
81
A
THR
82
n
86
THR
82
A
ARG
83
n
87
ARG
83
A
THR
84
n
88
THR
84
A
GLY
85
n
89
GLY
85
A
THR
86
n
90
THR
86
A
GLU
87
n
91
GLU
87
A
PHE
88
n
92
PHE
88
A
PHE
89
n
93
PHE
89
A
SER
90
n
94
SER
90
A
ALA
91
n
95
ALA
91
A
LEU
92
n
96
LEU
92
A
THR
93
n
97
THR
93
A
ASP
94
n
98
ASP
94
A
TYR
95
n
99
TYR
95
A
ALA
96
n
100
ALA
96
A
THR
97
n
101
THR
97
A
GLN
98
n
102
GLN
98
A
GLN
99
n
103
GLN
99
A
ALA
100
n
104
ALA
100
A
GLY
101
n
105
GLY
101
A
LEU
102
n
106
LEU
102
A
PRO
103
n
107
PRO
103
A
ILE
104
n
108
ILE
104
A
THR
105
n
109
THR
105
A
PHE
106
n
110
PHE
106
A
SER
107
n
111
SER
107
A
ALA
108
n
112
ALA
108
A
4.4269
-1.5942
2.3137
0.7888
-0.6738
1.4161
-0.0228
0.1979
0.0400
-0.0179
-0.0117
-0.0330
-0.0082
0.1439
0.0344
0.0574
0.0069
0.0063
0.0854
0.0016
0.0585
refined
68.6596
55.7818
49.4496
X-RAY DIFFRACTION
1.1871
-0.2859
-0.3591
0.8720
0.2367
1.4734
-0.0208
0.0665
-0.0483
-0.0206
0.0472
-0.0521
0.1356
0.0908
-0.0263
0.0519
0.0257
0.0069
0.0554
-0.0111
0.0349
refined
69.5247
46.7606
45.2067
X-RAY DIFFRACTION
5.0352
0.1103
-2.3942
0.8526
2.2123
7.1880
-0.2670
-0.2424
-0.1394
0.1264
0.0956
0.0381
0.5004
0.4816
0.1714
0.1332
0.1120
0.0247
0.1307
0.0552
0.0434
refined
74.4595
40.5597
52.8845
X-RAY DIFFRACTION
A
0
A
26
X-RAY DIFFRACTION
1
A
27
A
90
X-RAY DIFFRACTION
2
A
91
A
108
X-RAY DIFFRACTION
3
author_and_software_defined_assembly
PISA
6
hexameric
16970
-174
23440
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
0.0000000000
1.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
5_555
z,x,y
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1.0000000000
0.0000000000
0.0000000000
9_555
y,z,x
crystal symmetry 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
14_666
-y+5/4,-x+5/4,-z+5/4
crystal symmetry operation
120.0250000000
120.0250000000
120.0250000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
19_666
-x+5/4,-z+5/4,-y+5/4
crystal symmetry operation
120.0250000000
120.0250000000
120.0250000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
24_666
-z+5/4,-y+5/4,-x+5/4
crystal symmetry operation
120.0250000000
120.0250000000
120.0250000000
A
N
GLU
34
A
N
GLU
38
A
O
THR
41
A
O
THR
45
A
N
LEU
42
A
N
LEU
46
A
O
ILE
50
A
O
ILE
54
A
N
ASN
53
A
N
ASN
57
A
O
TRP
62
A
O
TRP
66
A
N
ALA
65
A
N
ALA
69
A
O
GLY
68
A
O
GLY
72
A
N
ILE
75
A
N
ILE
79
A
O
GLU
78
A
O
GLU
82
1
A
NA
203
D
NA
1
A
SO4
204
E
SO4
1
A
SO4
204
E
SO4
1
A
HOH
302
F
HOH
1
A
HOH
311
F
HOH
1
A
HOH
328
F
HOH
1
A
HOH
343
F
HOH
1
A
HOH
412
F
HOH
1
A
OG
SER
0
A
OG
SER
4
1
Y
1
A
CG
ASP
28
A
CG
ASP
32
1
Y
1
A
OD1
ASP
28
A
OD1
ASP
32
1
Y
1
A
OD2
ASP
28
A
OD2
ASP
32
1
Y
1
A
CG
GLU
34
A
CG
GLU
38
1
Y
1
A
CD
GLU
34
A
CD
GLU
38
1
Y
1
A
OE1
GLU
34
A
OE1
GLU
38
1
Y
1
A
OE2
GLU
34
A
OE2
GLU
38
1
Y
1
A
CG
GLU
45
A
CG
GLU
49
1
Y
1
A
CD
GLU
45
A
CD
GLU
49
1
Y
1
A
OE1
GLU
45
A
OE1
GLU
49
1
Y
1
A
OE2
GLU
45
A
OE2
GLU
49
1
Y
1
A
CG
LYS
49
A
CG
LYS
53
1
Y
1
A
CD
LYS
49
A
CD
LYS
53
1
Y
1
A
CE
LYS
49
A
CE
LYS
53
1
Y
1
A
NZ
LYS
49
A
NZ
LYS
53
1
Y
1
A
GLY
-3
A
GLY
1
1
Y
1
A
PRO
-2
A
PRO
2
1
Y
1
A
GLY
-1
A
GLY
3
1
Y
1
A
A
O
O
HOH
HOH
403
403
2.16
1_555
13_545
55.810
18.3399
4.430
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.9550
0.9390
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.1959
0.1624
0.1640
1.9000
42.9800
584
11700
4.8000
98.4100
0.1688
0.1405
1.000
0.330
0.8886
3.8890
0.0620
0.1130
0.1108
RANDOM
1
THROUGHOUT
0.000
MOLECULAR REPLACEMENT
0.1130
0.1110
0.8000
0.8000
1.2000
PDB entry 1EW4
MAXIMUM LIKELIHOOD
MASK
1.9000
42.9800
115
961
14
0
832
0.011
0.019
898
0.001
0.020
821
1.349
1.948
1234
0.775
3.000
1882
5.785
5.000
122
37.008
24.186
43
11.243
15.000
135
13.889
15.000
6
0.083
0.200
142
0.006
0.020
1060
0.001
0.020
214
0.895
0.893
451
0.869
0.883
448
1.548
1.314
563
0.2280
0.1860
1.9490
36
805
841
20
93.6500
20.707
1.90
42.9800
4JPD
11700
-3.000
0.111
1
21.420
100.000
0.437
1.90
2.000
6.750
11845
836
1
100.000
0.374
2.000
2.060
7.890
11425
800
1
100.000
0.306
2.060
2.120
9.740
11224
787
1
100.000
0.274
2.120
2.180
10.860
10931
770
1
100.000
0.229
2.180
2.250
12.840
10432
738
1
100.000
0.211
2.250
2.330
13.740
10496
739
1
100.000
0.188
2.330
2.420
14.980
9785
694
1
100.000
0.165
2.420
2.520
17.350
9445
671
1
100.000
0.147
2.520
2.630
18.970
9168
650
1
100.000
0.136
2.630
2.760
19.870
8790
629
1
100.000
0.106
2.760
2.910
25.100
8438
603
1
100.000
0.092
2.910
3.080
27.500
7822
566
1
100.000
0.081
3.080
3.300
30.790
7418
539
1
100.000
0.063
3.300
3.560
37.770
6814
504
1
100.000
0.058
3.560
3.900
39.340
6208
462
1
100.000
0.050
3.900
4.360
43.370
5701
440
1
100.000
0.046
4.360
5.040
47.910
5029
380
1
100.000
0.060
5.040
6.170
37.290
4349
337
1
100.000
0.050
6.170
8.720
40.840
3380
273
1
100.000
data scaling
Wolfgang Kabsch
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html
XSCALE
package
phasing
Randy J. Read
cimr-phaser@lists.cam.ac.uk
Mon Oct 8 13:56:31 2012 (svn )
http://www-structmed.cimr.cam.ac.uk/phaser/
PHASER
program
2.5.2
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
data extraction
PDB
deposit@deposit.rcsb.org
April 22, 2011
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.11
data reduction
XDS
The structure of CyaY from Burkholderia cenocepacia
1
N
N
2
N
N
2
N
N
3
N
N
4
N
N
5
N
N
A
ASP
3
A
ASP
7
HELX_P
A
GLY
27
A
GLY
31
1
1
25
A
PRO
56
A
PRO
60
HELX_P
A
MET
58
A
MET
62
5
2
3
A
GLU
87
A
GLU
91
HELX_P
A
GLY
101
A
GLY
105
1
3
15
METAL BINDING PROTEIN
SSGCID, Seattle Structural Genomics Center for Infectious Disease, CyaY, Frataxin, iron binding protein, METAL BINDING PROTEIN
CYAY_BURCJ
UNP
1
1
B4E5Z6
MSDTEYLARAEAVLAAVERTVDVANDGDHDIDLERNGSVLTLTFENGSKIIVNLQPPMKEVWIAAKAGGFHYRFIDGEWR
DTRTGTEFFSALTDYATQQAGLPITFSA
1
108
4JPD
1
108
B4E5Z6
A
1
5
112
1
expression tag
GLY
-3
4JPD
A
B4E5Z6
UNP
1
1
expression tag
PRO
-2
4JPD
A
B4E5Z6
UNP
2
1
expression tag
GLY
-1
4JPD
A
B4E5Z6
UNP
3
1
expression tag
SER
0
4JPD
A
B4E5Z6
UNP
4
6
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ASP
32
A
ASP
36
A
ASN
36
A
ASN
40
A
VAL
39
A
VAL
43
A
THR
43
A
THR
47
A
LYS
49
A
LYS
53
A
GLN
55
A
GLN
59
A
GLU
60
A
GLU
64
A
ALA
65
A
ALA
69
A
GLY
68
A
GLY
72
A
ILE
75
A
ILE
79
A
GLU
78
A
GLU
82
A
ASP
81
A
ASP
85
BINDING SITE FOR RESIDUE ACT A 201
A
ACT
201
Software
7
BINDING SITE FOR RESIDUE ACT A 202
A
ACT
202
Software
6
BINDING SITE FOR RESIDUE NA A 203
A
NA
203
Software
3
BINDING SITE FOR RESIDUE SO4 A 204
A
SO4
204
Software
9
A
HIS
29
A
HIS
33
7
1_555
A
ASP
30
A
ASP
34
7
1_555
A
ILE
31
A
ILE
35
7
1_555
A
PHE
44
A
PHE
48
7
1_555
A
GLU
45
A
GLU
49
7
1_555
A
ALA
100
A
ALA
104
7
1_555
A
HOH
320
F
HOH
7
1_555
A
HIS
71
A
HIS
75
6
1_555
A
THR
82
A
THR
86
6
1_555
A
ARG
83
A
ARG
87
6
1_555
A
ARG
83
A
ARG
87
6
13_545
A
HOH
313
F
HOH
6
13_545
A
HOH
351
F
HOH
6
1_555
A
GLY
77
A
GLY
81
3
5_555
A
GLY
77
A
GLY
81
3
9_555
A
GLY
77
A
GLY
81
3
1_555
A
ARG
9
A
ARG
13
9
1_555
A
ARG
9
A
ARG
13
9
9_555
A
ARG
9
A
ARG
13
9
5_555
A
HOH
370
F
HOH
9
9_555
A
HOH
370
F
HOH
9
1_555
A
HOH
370
F
HOH
9
5_555
A
HOH
374
F
HOH
9
1_555
A
HOH
374
F
HOH
9
5_555
A
HOH
374
F
HOH
9
9_555
212
P 43 3 2