0.024784
0.000000
0.013084
0.000000
0.015490
0.000000
0.000000
0.000000
0.027249
0.00000
0.00000
0.00000
David, G.
Blondeau, K.
Renouard, M.
Penel, S.
Lewit-Bentley, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.00
117.83
90.00
40.348
64.558
41.499
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 S
149.211
y
METHIONINE
L-peptide linking
Ni 2
58.693
NICKEL (II) 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
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
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
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
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
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
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
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
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
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
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
NI
N
251
N
N
N
252
S
C
N
253
N
C
N
254
N
O
N
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
Y
261
N
C
N
262
N
O
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
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
N
N
275
S
C
N
276
N
C
N
277
N
O
N
278
N
C
N
279
N
C
N
280
N
C
N
281
N
O
N
282
N
H
N
283
N
H
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
N
C
N
296
N
O
N
297
N
O
N
298
N
H
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
N
N
306
S
C
N
307
N
C
N
308
N
O
N
309
R
C
N
310
N
O
N
311
N
C
N
312
N
O
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
H
N
321
N
H
N
322
N
N
N
323
S
C
N
324
N
C
N
325
N
O
N
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
C
Y
330
N
N
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
C
Y
335
N
C
N
336
N
O
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
H
N
348
N
H
N
349
N
N
N
350
S
C
N
351
N
C
N
352
N
O
N
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
Y
359
N
C
N
360
N
O
N
361
N
O
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
H
N
372
N
H
N
373
N
N
N
374
S
C
N
375
N
C
N
376
N
O
N
377
N
C
N
378
N
C
N
379
N
C
N
380
N
O
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
390
N
H
N
391
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
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
N
90
N
sing
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
doub
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
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
doub
N
109
N
sing
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
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
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
doub
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
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
doub
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
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
doub
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
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
doub
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
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
doub
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
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
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
doub
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
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
doub
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
sing
N
310
N
sing
N
311
N
sing
N
312
N
doub
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
Y
317
N
doub
Y
318
N
sing
Y
319
N
sing
N
320
N
sing
Y
321
N
doub
Y
322
N
sing
Y
323
N
sing
N
324
N
sing
Y
325
N
sing
Y
326
N
doub
N
327
N
sing
Y
328
N
doub
N
329
N
sing
Y
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
sing
N
338
N
sing
N
339
N
sing
N
340
N
doub
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
Y
345
N
doub
Y
346
N
sing
Y
347
N
sing
N
348
N
sing
Y
349
N
doub
N
350
N
sing
Y
351
N
doub
N
352
N
sing
Y
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
N
363
N
sing
N
364
N
doub
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
N
373
N
sing
N
374
N
sing
N
375
N
sing
US
J.Biol.Chem.
JBCHA3
0071
0021-9258
278
43728
10.1074/JBC.M304484200
12909634
Yoda from Escherichia Coli is a Metal-Binding, Lipocalin-Like Protein
2003
10.2210/pdb1oej/pdb
pdb_00001oej
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
MIRRORS
CCD
2001-02-15
MARRESEARCH
SI 111
SINGLE WAVELENGTH
M
x-ray
1
1.3
1.0
PX9.5
SRS
1.3
SYNCHROTRON
SRS BEAMLINE PX9.5
22373.879
HYPOTHETICAL PROTEIN YODA
1
nat
polymer
58.693
NICKEL (II) ION
1
syn
non-polymer
18.015
water
101
nat
water
no
no
HGHHSHGKPLTEVEQKAANGVFDDANVQNRTLSDWDGVWQSVYPLLQSGKLDPVFQKKADADKTKTFAEIKDYYHKGYAT
DIEMIGIEDGIVEFHRNNETTSCKYDYDGYKILTYKSGKKGVRYLFECKDPESKAPKYIQFSDHIIAPRKSSHFHIFMGN
DSQQSLLNEMENWPTYYPYQLSSEEVVEEMMSH
HGHHSHGKPLTEVEQKAANGVFDDANVQNRTLSDWDGVWQSVYPLLQSGKLDPVFQKKADADKTKTFAEIKDYYHKGYAT
DIEMIGIEDGIVEFHRNNETTSCKYDYDGYKILTYKSGKKGVRYLFECKDPESKAPKYIQFSDHIIAPRKSSHFHIFMGN
DSQQSLLNEMENWPTYYPYQLSSEEVVEEMMSH
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
sample
562
ESCHERICHIA COLI
1
2.17
43
6.50
10 MG/ML PROTEIN, 30% PEG 10000, 100 MM SODIUM CACODYLATE, PH = 6.5 200 MM SODIUM ACETATE
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_status
pdbx_initial_refinement_model
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Other
Refinement description
1
0
2003-08-15
1
1
2011-05-08
1
2
2011-07-13
1
3
2023-12-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_sf
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
YODA FROM ESCHERICHIA COLI CRYSTALLISED WITH CADMIUM IONS
YODA FROM ESCHERICHIA COLI CRYSTALLISED WITH ZINC IONS
PDBE
Y
PDBE
2003-03-27
REL
REL
NI
NICKEL (II) ION
HOH
water
THE SEQUENCE: MAIRLYKLAVALGVFIVSAPAFS
THAT IS INCLUDED THE SWISPROT RECORD
UPSTREAM OF THE SEQUENCE CRYSTALLISED,
CORRESPONDS TO A SIGNAL SEQUENCE THAT
IS CLEAVED IN THE MATURE PROTEIN.
1OEE
PDB ENTRY 1OEE
PDB
experimental model
NI
1194
2
NI
NI
1194
A
HOH
2001
3
HOH
HOH
2001
A
HOH
2002
3
HOH
HOH
2002
A
HOH
2003
3
HOH
HOH
2003
A
HOH
2004
3
HOH
HOH
2004
A
HOH
2005
3
HOH
HOH
2005
A
HOH
2006
3
HOH
HOH
2006
A
HOH
2007
3
HOH
HOH
2007
A
HOH
2008
3
HOH
HOH
2008
A
HOH
2009
3
HOH
HOH
2009
A
HOH
2010
3
HOH
HOH
2010
A
HOH
2011
3
HOH
HOH
2011
A
HOH
2012
3
HOH
HOH
2012
A
HOH
2013
3
HOH
HOH
2013
A
HOH
2014
3
HOH
HOH
2014
A
HOH
2015
3
HOH
HOH
2015
A
HOH
2016
3
HOH
HOH
2016
A
HOH
2017
3
HOH
HOH
2017
A
HOH
2018
3
HOH
HOH
2018
A
HOH
2019
3
HOH
HOH
2019
A
HOH
2020
3
HOH
HOH
2020
A
HOH
2021
3
HOH
HOH
2021
A
HOH
2022
3
HOH
HOH
2022
A
HOH
2023
3
HOH
HOH
2023
A
HOH
2024
3
HOH
HOH
2024
A
HOH
2025
3
HOH
HOH
2025
A
HOH
2026
3
HOH
HOH
2026
A
HOH
2027
3
HOH
HOH
2027
A
HOH
2028
3
HOH
HOH
2028
A
HOH
2029
3
HOH
HOH
2029
A
HOH
2030
3
HOH
HOH
2030
A
HOH
2031
3
HOH
HOH
2031
A
HOH
2032
3
HOH
HOH
2032
A
HOH
2033
3
HOH
HOH
2033
A
HOH
2034
3
HOH
HOH
2034
A
HOH
2035
3
HOH
HOH
2035
A
HOH
2036
3
HOH
HOH
2036
A
HOH
2037
3
HOH
HOH
2037
A
HOH
2038
3
HOH
HOH
2038
A
HOH
2039
3
HOH
HOH
2039
A
HOH
2040
3
HOH
HOH
2040
A
HOH
2041
3
HOH
HOH
2041
A
HOH
2042
3
HOH
HOH
2042
A
HOH
2043
3
HOH
HOH
2043
A
HOH
2044
3
HOH
HOH
2044
A
HOH
2045
3
HOH
HOH
2045
A
HOH
2046
3
HOH
HOH
2046
A
HOH
2047
3
HOH
HOH
2047
A
HOH
2048
3
HOH
HOH
2048
A
HOH
2049
3
HOH
HOH
2049
A
HOH
2050
3
HOH
HOH
2050
A
HOH
2051
3
HOH
HOH
2051
A
HOH
2052
3
HOH
HOH
2052
A
HOH
2053
3
HOH
HOH
2053
A
HOH
2054
3
HOH
HOH
2054
A
HOH
2055
3
HOH
HOH
2055
A
HOH
2056
3
HOH
HOH
2056
A
HOH
2057
3
HOH
HOH
2057
A
HOH
2058
3
HOH
HOH
2058
A
HOH
2059
3
HOH
HOH
2059
A
HOH
2060
3
HOH
HOH
2060
A
HOH
2061
3
HOH
HOH
2061
A
HOH
2062
3
HOH
HOH
2062
A
HOH
2063
3
HOH
HOH
2063
A
HOH
2064
3
HOH
HOH
2064
A
HOH
2065
3
HOH
HOH
2065
A
HOH
2066
3
HOH
HOH
2066
A
HOH
2067
3
HOH
HOH
2067
A
HOH
2068
3
HOH
HOH
2068
A
HOH
2069
3
HOH
HOH
2069
A
HOH
2070
3
HOH
HOH
2070
A
HOH
2071
3
HOH
HOH
2071
A
HOH
2072
3
HOH
HOH
2072
A
HOH
2073
3
HOH
HOH
2073
A
HOH
2074
3
HOH
HOH
2074
A
HOH
2075
3
HOH
HOH
2075
A
HOH
2076
3
HOH
HOH
2076
A
HOH
2077
3
HOH
HOH
2077
A
HOH
2078
3
HOH
HOH
2078
A
HOH
2079
3
HOH
HOH
2079
A
HOH
2080
3
HOH
HOH
2080
A
HOH
2081
3
HOH
HOH
2081
A
HOH
2082
3
HOH
HOH
2082
A
HOH
2083
3
HOH
HOH
2083
A
HOH
2084
3
HOH
HOH
2084
A
HOH
2085
3
HOH
HOH
2085
A
HOH
2086
3
HOH
HOH
2086
A
HOH
2087
3
HOH
HOH
2087
A
HOH
2088
3
HOH
HOH
2088
A
HOH
2089
3
HOH
HOH
2089
A
HOH
2090
3
HOH
HOH
2090
A
HOH
2091
3
HOH
HOH
2091
A
HOH
2092
3
HOH
HOH
2092
A
HOH
2093
3
HOH
HOH
2093
A
HOH
2094
3
HOH
HOH
2094
A
HOH
2095
3
HOH
HOH
2095
A
HOH
2096
3
HOH
HOH
2096
A
HOH
2097
3
HOH
HOH
2097
A
HOH
2098
3
HOH
HOH
2098
A
HOH
2099
3
HOH
HOH
2099
A
HOH
2100
3
HOH
HOH
2100
A
HOH
2101
3
HOH
HOH
2101
A
n
1
1
A
n
2
2
A
n
3
3
A
n
4
4
A
n
5
5
A
n
6
6
A
GLY
7
n
7
GLY
7
A
LYS
8
n
8
LYS
8
A
PRO
9
n
9
PRO
9
A
LEU
10
n
10
LEU
10
A
THR
11
n
11
THR
11
A
GLU
12
n
12
GLU
12
A
VAL
13
n
13
VAL
13
A
GLU
14
n
14
GLU
14
A
GLN
15
n
15
GLN
15
A
LYS
16
n
16
LYS
16
A
ALA
17
n
17
ALA
17
A
ALA
18
n
18
ALA
18
A
ASN
19
n
19
ASN
19
A
GLY
20
n
20
GLY
20
A
VAL
21
n
21
VAL
21
A
PHE
22
n
22
PHE
22
A
ASP
23
n
23
ASP
23
A
ASP
24
n
24
ASP
24
A
ALA
25
n
25
ALA
25
A
ASN
26
n
26
ASN
26
A
VAL
27
n
27
VAL
27
A
GLN
28
n
28
GLN
28
A
ASN
29
n
29
ASN
29
A
ARG
30
n
30
ARG
30
A
THR
31
n
31
THR
31
A
LEU
32
n
32
LEU
32
A
SER
33
n
33
SER
33
A
ASP
34
n
34
ASP
34
A
TRP
35
n
35
TRP
35
A
ASP
36
n
36
ASP
36
A
GLY
37
n
37
GLY
37
A
VAL
38
n
38
VAL
38
A
TRP
39
n
39
TRP
39
A
GLN
40
n
40
GLN
40
A
SER
41
n
41
SER
41
A
VAL
42
n
42
VAL
42
A
TYR
43
n
43
TYR
43
A
PRO
44
n
44
PRO
44
A
LEU
45
n
45
LEU
45
A
LEU
46
n
46
LEU
46
A
GLN
47
n
47
GLN
47
A
SER
48
n
48
SER
48
A
GLY
49
n
49
GLY
49
A
LYS
50
n
50
LYS
50
A
LEU
51
n
51
LEU
51
A
ASP
52
n
52
ASP
52
A
PRO
53
n
53
PRO
53
A
VAL
54
n
54
VAL
54
A
PHE
55
n
55
PHE
55
A
GLN
56
n
56
GLN
56
A
LYS
57
n
57
LYS
57
A
LYS
58
n
58
LYS
58
A
ALA
59
n
59
ALA
59
A
ASP
60
n
60
ASP
60
A
ALA
61
n
61
ALA
61
A
ASP
62
n
62
ASP
62
A
LYS
63
n
63
LYS
63
A
THR
64
n
64
THR
64
A
LYS
65
n
65
LYS
65
A
THR
66
n
66
THR
66
A
PHE
67
n
67
PHE
67
A
ALA
68
n
68
ALA
68
A
GLU
69
n
69
GLU
69
A
ILE
70
n
70
ILE
70
A
LYS
71
n
71
LYS
71
A
ASP
72
n
72
ASP
72
A
TYR
73
n
73
TYR
73
A
TYR
74
n
74
TYR
74
A
HIS
75
n
75
HIS
75
A
LYS
76
n
76
LYS
76
A
GLY
77
n
77
GLY
77
A
TYR
78
n
78
TYR
78
A
ALA
79
n
79
ALA
79
A
THR
80
n
80
THR
80
A
ASP
81
n
81
ASP
81
A
ILE
82
n
82
ILE
82
A
GLU
83
n
83
GLU
83
A
MET
84
n
84
MET
84
A
ILE
85
n
85
ILE
85
A
GLY
86
n
86
GLY
86
A
ILE
87
n
87
ILE
87
A
GLU
88
n
88
GLU
88
A
ASP
89
n
89
ASP
89
A
GLY
90
n
90
GLY
90
A
ILE
91
n
91
ILE
91
A
VAL
92
n
92
VAL
92
A
GLU
93
n
93
GLU
93
A
PHE
94
n
94
PHE
94
A
HIS
95
n
95
HIS
95
A
ARG
96
n
96
ARG
96
A
ASN
97
n
97
ASN
97
A
ASN
98
n
98
ASN
98
A
GLU
99
n
99
GLU
99
A
THR
100
n
100
THR
100
A
THR
101
n
101
THR
101
A
SER
102
n
102
SER
102
A
CYS
103
n
103
CYS
103
A
LYS
104
n
104
LYS
104
A
TYR
105
n
105
TYR
105
A
ASP
106
n
106
ASP
106
A
TYR
107
n
107
TYR
107
A
ASP
108
n
108
ASP
108
A
GLY
109
n
109
GLY
109
A
TYR
110
n
110
TYR
110
A
LYS
111
n
111
LYS
111
A
ILE
112
n
112
ILE
112
A
LEU
113
n
113
LEU
113
A
THR
114
n
114
THR
114
A
TYR
115
n
115
TYR
115
A
LYS
116
n
116
LYS
116
A
SER
117
n
117
SER
117
A
GLY
118
n
118
GLY
118
A
LYS
119
n
119
LYS
119
A
LYS
120
n
120
LYS
120
A
GLY
121
n
121
GLY
121
A
VAL
122
n
122
VAL
122
A
ARG
123
n
123
ARG
123
A
TYR
124
n
124
TYR
124
A
LEU
125
n
125
LEU
125
A
PHE
126
n
126
PHE
126
A
GLU
127
n
127
GLU
127
A
CYS
128
n
128
CYS
128
A
LYS
129
n
129
LYS
129
A
ASP
130
n
130
ASP
130
A
PRO
131
n
131
PRO
131
A
GLU
132
n
132
GLU
132
A
SER
133
n
133
SER
133
A
LYS
134
n
134
LYS
134
A
ALA
135
n
135
ALA
135
A
PRO
136
n
136
PRO
136
A
LYS
137
n
137
LYS
137
A
TYR
138
n
138
TYR
138
A
ILE
139
n
139
ILE
139
A
GLN
140
n
140
GLN
140
A
PHE
141
n
141
PHE
141
A
SER
142
n
142
SER
142
A
ASP
143
n
143
ASP
143
A
HIS
144
n
144
HIS
144
A
ILE
145
n
145
ILE
145
A
ILE
146
n
146
ILE
146
A
ALA
147
n
147
ALA
147
A
PRO
148
n
148
PRO
148
A
ARG
149
n
149
ARG
149
A
LYS
150
n
150
LYS
150
A
SER
151
n
151
SER
151
A
SER
152
n
152
SER
152
A
HIS
153
n
153
HIS
153
A
PHE
154
n
154
PHE
154
A
HIS
155
n
155
HIS
155
A
ILE
156
n
156
ILE
156
A
PHE
157
n
157
PHE
157
A
MET
158
n
158
MET
158
A
GLY
159
n
159
GLY
159
A
ASN
160
n
160
ASN
160
A
ASP
161
n
161
ASP
161
A
SER
162
n
162
SER
162
A
GLN
163
n
163
GLN
163
A
GLN
164
n
164
GLN
164
A
SER
165
n
165
SER
165
A
LEU
166
n
166
LEU
166
A
LEU
167
n
167
LEU
167
A
ASN
168
n
168
ASN
168
A
GLU
169
n
169
GLU
169
A
MET
170
n
170
MET
170
A
GLU
171
n
171
GLU
171
A
ASN
172
n
172
ASN
172
A
TRP
173
n
173
TRP
173
A
PRO
174
n
174
PRO
174
A
THR
175
n
175
THR
175
A
TYR
176
n
176
TYR
176
A
TYR
177
n
177
TYR
177
A
PRO
178
n
178
PRO
178
A
TYR
179
n
179
TYR
179
A
GLN
180
n
180
GLN
180
A
LEU
181
n
181
LEU
181
A
SER
182
n
182
SER
182
A
SER
183
n
183
SER
183
A
GLU
184
n
184
GLU
184
A
GLU
185
n
185
GLU
185
A
VAL
186
n
186
VAL
186
A
VAL
187
n
187
VAL
187
A
GLU
188
n
188
GLU
188
A
GLU
189
n
189
GLU
189
A
MET
190
n
190
MET
190
A
MET
191
n
191
MET
191
A
SER
192
n
192
SER
192
A
HIS
193
n
193
HIS
193
A
author_and_software_defined_assembly
PQS
1
monomeric
A
HIS
144
A
NE2
HIS
144
1_555
A
NI
1194
B
NI
NI
1_555
A
HIS
153
A
NE2
HIS
153
1_555
99.9
A
HIS
144
A
NE2
HIS
144
1_555
A
NI
1194
B
NI
NI
1_555
A
HIS
155
A
NE2
HIS
155
1_555
102.2
A
HIS
153
A
NE2
HIS
153
1_555
A
NI
1194
B
NI
NI
1_555
A
HIS
155
A
NE2
HIS
155
1_555
109.8
A
HIS
144
A
NE2
HIS
144
1_555
A
NI
1194
B
NI
NI
1_555
A
HOH
2091
C
O
HOH
1_555
127.1
A
HIS
153
A
NE2
HIS
153
1_555
A
NI
1194
B
NI
NI
1_555
A
HOH
2091
C
O
HOH
1_555
118.8
A
HIS
155
A
NE2
HIS
155
1_555
A
NI
1194
B
NI
NI
1_555
A
HOH
2091
C
O
HOH
1_555
97.1
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
CYS
103
A
N
CYS
103
A
O
VAL
92
A
O
VAL
92
A
N
HIS
95
A
N
HIS
95
A
O
MET
84
A
O
MET
84
A
N
ILE
87
A
N
ILE
87
A
O
GLY
37
A
O
GLY
37
A
N
GLN
40
A
N
GLN
40
A
O
TYR
177
A
O
TYR
177
A
N
TYR
176
A
N
TYR
176
A
O
PHE
154
A
O
PHE
154
A
N
GLY
159
A
N
GLY
159
A
O
TYR
138
A
O
TYR
138
A
N
PHE
141
A
N
PHE
141
A
O
TYR
124
A
O
TYR
124
A
N
GLU
127
A
N
GLU
127
A
O
ASP
106
A
O
ASP
106
1
A
HIS
1
A
HIS
1
1
Y
1
A
GLY
2
A
GLY
2
1
Y
1
A
HIS
3
A
HIS
3
1
Y
1
A
HIS
4
A
HIS
4
1
Y
1
A
SER
5
A
SER
5
1
Y
1
A
HIS
6
A
HIS
6
1
Y
1
7.04
0.90
118.30
125.34
A
A
A
CB
CG
OD2
ASP
ASP
ASP
34
34
34
N
1
6.21
0.90
118.30
124.51
A
A
A
CB
CG
OD2
ASP
ASP
ASP
161
161
161
N
1
A
ASN
97
-39.92
92.65
1
A
ASN
98
73.11
-12.17
1
A
ASP
143
-150.85
30.96
1
A
HIS
144
59.69
19.89
1
A
ARG
149
179.56
135.47
1
A
ASP
161
-91.12
-64.93
1
A
SER
192
-110.94
-103.77
27.508
-0.45
0.00
-0.52
0.83
0.00
-0.87
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FIRST 6 RESIDUES AT THE N-TERMINUS ARE DISORDERED
0.25226
0.180
0.18371
1.81
36.76
653
12128
5.1
74.27
4.702
0.138
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.199
0.189
PDB ENTRY 1OEE
1.81
36.76
101
1628
1
0
1526
20.107
1.810
14.920
1OEJ
6027
0.06000
1
10.5000
1.600
74.5
0.58800
1.81
1.91
1.600
1
1.60
69.7
data reduction
MOSFLM
data scaling
SCALA
phasing
AMoRE
phasing
CCP4
refinement
REFMAC
YodA from Escherichia coli crystallised with no added ions
1
N
N
2
N
N
3
N
N
A
THR
11
A
THR
11
HELX_P
A
ASN
19
A
ASN
19
1
1
9
A
ASP
23
A
ASP
23
HELX_P
A
VAL
27
A
VAL
27
5
2
5
A
THR
31
A
THR
31
HELX_P
A
ASP
36
A
ASP
36
5
3
6
A
VAL
42
A
VAL
42
HELX_P
A
SER
48
A
SER
48
1
4
7
A
LEU
51
A
LEU
51
HELX_P
A
ASP
62
A
ASP
62
1
5
12
A
THR
66
A
THR
66
HELX_P
A
ALA
79
A
ALA
79
1
6
14
A
SER
162
A
SER
162
HELX_P
A
GLU
169
A
GLU
169
1
7
8
A
SER
182
A
SER
182
HELX_P
A
SER
192
A
SER
192
1
8
11
disulf
2.002
A
CYS
103
A
SG
CYS
103
1_555
A
CYS
128
A
SG
CYS
128
1_555
metalc
2.256
A
HIS
144
A
NE2
HIS
144
1_555
A
NI
1194
B
NI
NI
1_555
metalc
2.256
A
HIS
153
A
NE2
HIS
153
1_555
A
NI
1194
B
NI
NI
1_555
metalc
2.160
A
HIS
155
A
NE2
HIS
155
1_555
A
NI
1194
B
NI
NI
1_555
metalc
2.501
A
NI
1194
B
NI
NI
1_555
A
HOH
2091
C
O
HOH
1_555
STRESS PROTEIN/LIPOCALIN
STRESS PROTEIN/LIPOCALIN, STRESS PROTEIN, LIPOCALIN, YODA, STRESS PROTEIN-LIPOCALIN complex
YODA_ECOLI
UNP
1
P76344
24
216
1OEJ
1
193
P76344
A
1
1
193
9
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
GLU
99
A
GLU
99
A
LYS
104
A
LYS
104
A
ILE
91
A
ILE
91
A
ARG
96
A
ARG
96
A
MET
84
A
MET
84
A
GLU
88
A
GLU
88
A
GLY
37
A
GLY
37
A
SER
41
A
SER
41
A
THR
175
A
THR
175
A
PRO
178
A
PRO
178
A
PHE
154
A
PHE
154
A
GLY
159
A
GLY
159
A
TYR
138
A
TYR
138
A
SER
142
A
SER
142
A
LYS
120
A
LYS
120
A
GLU
127
A
GLU
127
A
ASP
106
A
ASP
106
A
THR
114
A
THR
114
BINDING SITE FOR RESIDUE NI A1194
Software
4
A
HIS
144
A
HIS
144
4
1_555
A
HIS
153
A
HIS
153
4
1_555
A
HIS
155
A
HIS
155
4
1_555
A
HOH
2091
C
HOH
4
1_555
4
P 1 21 1