0.023697
0.000000
0.000000
0.000000
0.019079
0.000000
0.000000
0.000000
0.018156
0.00000
0.00000
0.00000
Osipiuk, J.
Maltseva, N.
Dementieva, I.
Moy, S.
Joachimiak, A.
Midwest Center for Structural Genomics (MCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
42.200
52.415
55.079
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
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
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
N
N
170
S
C
N
171
N
C
N
172
N
O
N
173
N
C
N
174
N
C
N
175
N
C
N
176
N
C
N
177
N
O
N
178
N
H
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
N
N
192
S
C
N
193
N
C
N
194
N
O
N
195
N
C
N
196
N
C
N
197
N
C
N
198
N
C
N
199
N
N
N
200
N
O
N
201
N
H
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
N
N
217
S
C
N
218
N
C
N
219
N
O
N
220
N
C
N
221
N
C
N
222
N
S
N
223
N
C
N
224
N
O
N
225
N
H
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
NI
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
To be Published
0353
X-ray crystal structure of YpmB protein from Bacillus subtilis.
10.2210/pdb2gu3/pdb
pdb_00002gu3
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
2006-04-19
SBC-3
double crystal monochromator
MAD
M
x-ray
1
0.97872
1.0
1.48520
1.0
1.48590
1.0
1.45180
1.0
19-BM
APS
0.97872, 1.48520, 1.48590, 1.45180
SYNCHROTRON
APS BEAMLINE 19-BM
15055.077
YpmB protein
1
man
polymer
58.693
NICKEL (II) ION
1
syn
non-polymer
18.015
water
145
nat
water
no
no
SNASAMAQKEEGHEAAAAEAKKETDLAHVDQVETFVGKEKYYVVKGTDKKGTALYVWVPADKKAKILSKEAKEGISEDKA
AKIIKDEGLVSKQKEVHLAREGNVLLWEVTYLDKEGQYSLSYVDFTTGKILKNITP
SNASAMAQKEEGHEAAAAEAKKETDLAHVDQVETFVGKEKYYVVKGTDKKGTALYVWVPADKKAKILSKEAKEGISEDKA
AKIIKDEGLVSKQKEVHLAREGNVLLWEVTYLDKEGQYSLSYVDFTTGKILKNITP
A
APC1927
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
Bacillus
Bacillus subtilis
subsp. subtilis str. 168
Escherichia
Escherichia coli
sample
ypmB, BSU22380
224308
Bacillus subtilis subsp. subtilis str. 168
469008
Escherichia coli BL21(DE3)
BL21(DE3)
plasmid
pMCSG7
1
2.02
39.19
VAPOR DIFFUSION, HANGING DROP
8.5
10 mM nickel chloride, 25% PEG 2000 MME, 100 mM Tris buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
295
Midwest Center for Structural Genomics
MCSG
PSI, Protein Structure Initiative
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Advisory
Version format compliance
Data collection
Database references
Derived calculations
1
0
2006-05-30
1
1
2008-05-01
1
2
2011-07-13
1
3
2024-02-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr1_symmetry
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.ptnr3_symmetry
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_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.ptnr1_symmetry
_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
_struct_conn.ptnr2_symmetry
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC
ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL
UNIT OF THIS PROTEIN IS UNKNOWN.
Y
RCSB
Y
RCSB
2006-04-28
REL
REL
NI
NICKEL (II) ION
HOH
water
NI
201
2
NI
NI
201
A
HOH
1
3
HOH
HOH
202
A
HOH
2
3
HOH
HOH
203
A
HOH
3
3
HOH
HOH
204
A
HOH
4
3
HOH
HOH
205
A
HOH
5
3
HOH
HOH
206
A
HOH
6
3
HOH
HOH
207
A
HOH
7
3
HOH
HOH
208
A
HOH
8
3
HOH
HOH
209
A
HOH
9
3
HOH
HOH
210
A
HOH
10
3
HOH
HOH
211
A
HOH
11
3
HOH
HOH
212
A
HOH
12
3
HOH
HOH
213
A
HOH
13
3
HOH
HOH
214
A
HOH
14
3
HOH
HOH
215
A
HOH
15
3
HOH
HOH
216
A
HOH
16
3
HOH
HOH
217
A
HOH
17
3
HOH
HOH
218
A
HOH
18
3
HOH
HOH
219
A
HOH
19
3
HOH
HOH
220
A
HOH
20
3
HOH
HOH
221
A
HOH
21
3
HOH
HOH
222
A
HOH
22
3
HOH
HOH
223
A
HOH
23
3
HOH
HOH
224
A
HOH
24
3
HOH
HOH
225
A
HOH
25
3
HOH
HOH
226
A
HOH
26
3
HOH
HOH
227
A
HOH
27
3
HOH
HOH
228
A
HOH
28
3
HOH
HOH
229
A
HOH
29
3
HOH
HOH
230
A
HOH
30
3
HOH
HOH
231
A
HOH
31
3
HOH
HOH
232
A
HOH
32
3
HOH
HOH
233
A
HOH
33
3
HOH
HOH
234
A
HOH
34
3
HOH
HOH
235
A
HOH
35
3
HOH
HOH
236
A
HOH
36
3
HOH
HOH
237
A
HOH
37
3
HOH
HOH
238
A
HOH
38
3
HOH
HOH
239
A
HOH
39
3
HOH
HOH
240
A
HOH
40
3
HOH
HOH
241
A
HOH
41
3
HOH
HOH
242
A
HOH
42
3
HOH
HOH
243
A
HOH
43
3
HOH
HOH
244
A
HOH
44
3
HOH
HOH
245
A
HOH
45
3
HOH
HOH
246
A
HOH
46
3
HOH
HOH
247
A
HOH
47
3
HOH
HOH
248
A
HOH
48
3
HOH
HOH
249
A
HOH
49
3
HOH
HOH
250
A
HOH
50
3
HOH
HOH
251
A
HOH
51
3
HOH
HOH
252
A
HOH
52
3
HOH
HOH
253
A
HOH
53
3
HOH
HOH
254
A
HOH
54
3
HOH
HOH
255
A
HOH
55
3
HOH
HOH
256
A
HOH
56
3
HOH
HOH
257
A
HOH
57
3
HOH
HOH
258
A
HOH
58
3
HOH
HOH
259
A
HOH
59
3
HOH
HOH
260
A
HOH
60
3
HOH
HOH
261
A
HOH
61
3
HOH
HOH
262
A
HOH
62
3
HOH
HOH
263
A
HOH
63
3
HOH
HOH
264
A
HOH
64
3
HOH
HOH
265
A
HOH
65
3
HOH
HOH
266
A
HOH
66
3
HOH
HOH
267
A
HOH
67
3
HOH
HOH
268
A
HOH
68
3
HOH
HOH
269
A
HOH
69
3
HOH
HOH
270
A
HOH
70
3
HOH
HOH
271
A
HOH
71
3
HOH
HOH
272
A
HOH
72
3
HOH
HOH
273
A
HOH
73
3
HOH
HOH
274
A
HOH
74
3
HOH
HOH
275
A
HOH
75
3
HOH
HOH
276
A
HOH
76
3
HOH
HOH
277
A
HOH
77
3
HOH
HOH
278
A
HOH
78
3
HOH
HOH
279
A
HOH
79
3
HOH
HOH
280
A
HOH
80
3
HOH
HOH
281
A
HOH
81
3
HOH
HOH
282
A
HOH
82
3
HOH
HOH
283
A
HOH
83
3
HOH
HOH
284
A
HOH
84
3
HOH
HOH
285
A
HOH
85
3
HOH
HOH
286
A
HOH
86
3
HOH
HOH
287
A
HOH
87
3
HOH
HOH
288
A
HOH
88
3
HOH
HOH
289
A
HOH
89
3
HOH
HOH
290
A
HOH
90
3
HOH
HOH
291
A
HOH
91
3
HOH
HOH
292
A
HOH
92
3
HOH
HOH
293
A
HOH
93
3
HOH
HOH
294
A
HOH
94
3
HOH
HOH
295
A
HOH
95
3
HOH
HOH
296
A
HOH
96
3
HOH
HOH
297
A
HOH
97
3
HOH
HOH
298
A
HOH
98
3
HOH
HOH
299
A
HOH
99
3
HOH
HOH
300
A
HOH
100
3
HOH
HOH
301
A
HOH
101
3
HOH
HOH
302
A
HOH
102
3
HOH
HOH
303
A
HOH
103
3
HOH
HOH
304
A
HOH
104
3
HOH
HOH
305
A
HOH
105
3
HOH
HOH
306
A
HOH
106
3
HOH
HOH
307
A
HOH
107
3
HOH
HOH
308
A
HOH
108
3
HOH
HOH
309
A
HOH
109
3
HOH
HOH
310
A
HOH
110
3
HOH
HOH
311
A
HOH
111
3
HOH
HOH
312
A
HOH
112
3
HOH
HOH
313
A
HOH
113
3
HOH
HOH
314
A
HOH
114
3
HOH
HOH
315
A
HOH
115
3
HOH
HOH
316
A
HOH
116
3
HOH
HOH
317
A
HOH
117
3
HOH
HOH
318
A
HOH
118
3
HOH
HOH
319
A
HOH
119
3
HOH
HOH
320
A
HOH
120
3
HOH
HOH
321
A
HOH
121
3
HOH
HOH
322
A
HOH
122
3
HOH
HOH
323
A
HOH
123
3
HOH
HOH
324
A
HOH
124
3
HOH
HOH
325
A
HOH
125
3
HOH
HOH
326
A
HOH
126
3
HOH
HOH
327
A
HOH
127
3
HOH
HOH
328
A
HOH
128
3
HOH
HOH
329
A
HOH
129
3
HOH
HOH
330
A
HOH
130
3
HOH
HOH
331
A
HOH
131
3
HOH
HOH
332
A
HOH
132
3
HOH
HOH
333
A
HOH
133
3
HOH
HOH
334
A
HOH
134
3
HOH
HOH
335
A
HOH
135
3
HOH
HOH
336
A
HOH
136
3
HOH
HOH
337
A
HOH
137
3
HOH
HOH
338
A
HOH
138
3
HOH
HOH
339
A
HOH
139
3
HOH
HOH
340
A
HOH
140
3
HOH
HOH
341
A
HOH
141
3
HOH
HOH
342
A
HOH
142
3
HOH
HOH
343
A
HOH
143
3
HOH
HOH
344
A
HOH
144
3
HOH
HOH
345
A
HOH
145
3
HOH
HOH
346
A
n
1
26
A
n
2
27
A
n
3
28
A
n
4
29
A
n
5
30
A
n
6
31
A
n
7
32
A
n
8
33
A
LYS
34
n
9
LYS
34
A
GLU
35
n
10
GLU
35
A
GLU
36
n
11
GLU
36
A
GLY
37
n
12
GLY
37
A
HIS
38
n
13
HIS
38
A
GLU
39
n
14
GLU
39
A
ALA
40
n
15
ALA
40
A
ALA
41
n
16
ALA
41
A
ALA
42
n
17
ALA
42
A
ALA
43
n
18
ALA
43
A
GLU
44
n
19
GLU
44
A
ALA
45
n
20
ALA
45
A
LYS
46
n
21
LYS
46
A
LYS
47
n
22
LYS
47
A
GLU
48
n
23
GLU
48
A
THR
49
n
24
THR
49
A
ASP
50
n
25
ASP
50
A
LEU
51
n
26
LEU
51
A
ALA
52
n
27
ALA
52
A
HIS
53
n
28
HIS
53
A
VAL
54
n
29
VAL
54
A
ASP
55
n
30
ASP
55
A
GLN
56
n
31
GLN
56
A
VAL
57
n
32
VAL
57
A
GLU
58
n
33
GLU
58
A
THR
59
n
34
THR
59
A
PHE
60
n
35
PHE
60
A
VAL
61
n
36
VAL
61
A
GLY
62
n
37
GLY
62
A
LYS
63
n
38
LYS
63
A
GLU
64
n
39
GLU
64
A
LYS
65
n
40
LYS
65
A
TYR
66
n
41
TYR
66
A
TYR
67
n
42
TYR
67
A
VAL
68
n
43
VAL
68
A
VAL
69
n
44
VAL
69
A
LYS
70
n
45
LYS
70
A
GLY
71
n
46
GLY
71
A
THR
72
n
47
THR
72
A
ASP
73
n
48
ASP
73
A
LYS
74
n
49
LYS
74
A
LYS
75
n
50
LYS
75
A
GLY
76
n
51
GLY
76
A
THR
77
n
52
THR
77
A
ALA
78
n
53
ALA
78
A
LEU
79
n
54
LEU
79
A
TYR
80
n
55
TYR
80
A
VAL
81
n
56
VAL
81
A
TRP
82
n
57
TRP
82
A
VAL
83
n
58
VAL
83
A
PRO
84
n
59
PRO
84
A
ALA
85
n
60
ALA
85
A
ASP
86
n
61
ASP
86
A
LYS
87
n
62
LYS
87
A
LYS
88
n
63
LYS
88
A
ALA
89
n
64
ALA
89
A
LYS
90
n
65
LYS
90
A
ILE
91
n
66
ILE
91
A
LEU
92
n
67
LEU
92
A
SER
93
n
68
SER
93
A
LYS
94
n
69
LYS
94
A
GLU
95
n
70
GLU
95
A
ALA
96
n
71
ALA
96
A
LYS
97
n
72
LYS
97
A
GLU
98
n
73
GLU
98
A
GLY
99
n
74
GLY
99
A
ILE
100
n
75
ILE
100
A
SER
101
n
76
SER
101
A
GLU
102
n
77
GLU
102
A
ASP
103
n
78
ASP
103
A
LYS
104
n
79
LYS
104
A
ALA
105
n
80
ALA
105
A
ALA
106
n
81
ALA
106
A
LYS
107
n
82
LYS
107
A
ILE
108
n
83
ILE
108
A
ILE
109
n
84
ILE
109
A
LYS
110
n
85
LYS
110
A
ASP
111
n
86
ASP
111
A
GLU
112
n
87
GLU
112
A
GLY
113
n
88
GLY
113
A
LEU
114
n
89
LEU
114
A
VAL
115
n
90
VAL
115
A
SER
116
n
91
SER
116
A
LYS
117
n
92
LYS
117
A
GLN
118
n
93
GLN
118
A
LYS
119
n
94
LYS
119
A
GLU
120
n
95
GLU
120
A
VAL
121
n
96
VAL
121
A
HIS
122
n
97
HIS
122
A
LEU
123
n
98
LEU
123
A
ALA
124
n
99
ALA
124
A
ARG
125
n
100
ARG
125
A
GLU
126
n
101
GLU
126
A
GLY
127
n
102
GLY
127
A
ASN
128
n
103
ASN
128
A
VAL
129
n
104
VAL
129
A
LEU
130
n
105
LEU
130
A
LEU
131
n
106
LEU
131
A
TRP
132
n
107
TRP
132
A
GLU
133
n
108
GLU
133
A
VAL
134
n
109
VAL
134
A
THR
135
n
110
THR
135
A
TYR
136
n
111
TYR
136
A
LEU
137
n
112
LEU
137
A
ASP
138
n
113
ASP
138
A
LYS
139
n
114
LYS
139
A
GLU
140
n
115
GLU
140
A
GLY
141
n
116
GLY
141
A
GLN
142
n
117
GLN
142
A
TYR
143
n
118
TYR
143
A
SER
144
n
119
SER
144
A
LEU
145
n
120
LEU
145
A
SER
146
n
121
SER
146
A
TYR
147
n
122
TYR
147
A
VAL
148
n
123
VAL
148
A
ASP
149
n
124
ASP
149
A
PHE
150
n
125
PHE
150
A
THR
151
n
126
THR
151
A
THR
152
n
127
THR
152
A
GLY
153
n
128
GLY
153
A
LYS
154
n
129
LYS
154
A
ILE
155
n
130
ILE
155
A
LEU
156
n
131
LEU
156
A
LYS
157
n
132
LYS
157
A
ASN
158
n
133
ASN
158
A
ILE
159
n
134
ILE
159
A
THR
160
n
135
THR
160
A
PRO
161
n
136
PRO
161
A
1.9276
-0.1269
-0.2581
1.0520
-0.4930
0.9844
-0.0498
-0.0322
-0.1194
-0.0896
-0.0162
-0.1429
-0.0174
-0.0854
0.0660
-0.0483
-0.0122
0.0112
-0.0585
0.0081
-0.0380
refined
18.9556
27.4075
28.8769
X-RAY DIFFRACTION
A
34
A
9
A
161
A
136
X-RAY DIFFRACTION
1
author_defined_assembly
1
monomeric
A
HIS
53
A
NE2
HIS
28
1_555
A
NI
201
B
NI
NI
1_555
A
HIS
122
A
NE2
HIS
97
4_466
90.1
A
HIS
53
A
NE2
HIS
28
1_555
A
NI
201
B
NI
NI
1_555
A
HOH
219
C
O
HOH
4_466
110.0
A
HIS
122
A
NE2
HIS
97
4_466
A
NI
201
B
NI
NI
1_555
A
HOH
219
C
O
HOH
4_466
95.6
A
HIS
53
A
NE2
HIS
28
1_555
A
NI
201
B
NI
NI
1_555
A
HOH
264
C
O
HOH
1_555
172.6
A
HIS
122
A
NE2
HIS
97
4_466
A
NI
201
B
NI
NI
1_555
A
HOH
264
C
O
HOH
1_555
96.4
A
HOH
219
C
O
HOH
4_466
A
NI
201
B
NI
NI
1_555
A
HOH
264
C
O
HOH
1_555
73.1
A
HIS
53
A
NE2
HIS
28
1_555
A
NI
201
B
NI
NI
1_555
A
HOH
268
C
O
HOH
1_555
90.9
A
HIS
122
A
NE2
HIS
97
4_466
A
NI
201
B
NI
NI
1_555
A
HOH
268
C
O
HOH
1_555
176.1
A
HOH
219
C
O
HOH
4_466
A
NI
201
B
NI
NI
1_555
A
HOH
268
C
O
HOH
1_555
80.5
A
HOH
264
C
O
HOH
1_555
A
NI
201
B
NI
NI
1_555
A
HOH
268
C
O
HOH
1_555
82.9
A
HIS
53
A
NE2
HIS
28
1_555
A
NI
201
B
NI
NI
1_555
A
HOH
295
C
O
HOH
1_555
76.4
A
HIS
122
A
NE2
HIS
97
4_466
A
NI
201
B
NI
NI
1_555
A
HOH
295
C
O
HOH
1_555
86.2
A
HOH
219
C
O
HOH
4_466
A
NI
201
B
NI
NI
1_555
A
HOH
295
C
O
HOH
1_555
173.3
A
HOH
264
C
O
HOH
1_555
A
NI
201
B
NI
NI
1_555
A
HOH
295
C
O
HOH
1_555
100.4
A
HOH
268
C
O
HOH
1_555
A
NI
201
B
NI
NI
1_555
A
HOH
295
C
O
HOH
1_555
97.7
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
GLU
58
A
N
GLU
33
A
O
VAL
68
A
O
VAL
43
A
N
VAL
69
A
N
VAL
44
A
O
VAL
81
A
O
VAL
56
A
N
TRP
82
A
N
TRP
57
A
O
LEU
92
A
O
LEU
67
A
N
GLU
120
A
N
GLU
95
A
O
THR
135
A
O
THR
110
A
N
VAL
134
A
N
VAL
109
A
O
SER
146
A
O
SER
121
A
N
LEU
145
A
N
LEU
120
A
O
ILE
159
A
O
ILE
134
1
A
SER
26
A
SER
1
1
Y
1
A
ASN
27
A
ASN
2
1
Y
1
A
ALA
28
A
ALA
3
1
Y
1
A
SER
29
A
SER
4
1
Y
1
A
ALA
30
A
ALA
5
1
Y
1
A
MET
31
A
MET
6
1
Y
1
A
ALA
32
A
ALA
7
1
Y
1
A
GLN
33
A
GLN
8
1
Y
1
A
LYS
119
-114.20
-81.67
24.636
-1.29
0.00
0.00
0.76
0.00
0.53
0.958
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL DATA WERE USED IN FINAL ROUND OF
REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET.
0.2144
0.188
0.188
0.188
1.74
28.30
624
12750
12750
98.34
3.635
0.064
RANDOM
LIKELY RESIDUAL
1
0
0
MAD
0.125
0.80
0.80
1.20
MAXIMUM LIKELIHOOD
MASK
1.74
28.30
145
1154
1
0
1008
0.017
0.022
1037
1.576
1.975
1398
6.451
5.000
131
35.228
26.591
44
14.245
15.000
206
5.325
15.000
1
0.125
0.200
157
0.008
0.020
753
0.217
0.200
442
0.309
0.200
696
0.162
0.200
139
0.136
0.200
1
0.267
0.200
28
0.133
0.200
21
1.134
1.500
656
1.741
2.000
1027
2.869
3.000
437
4.261
4.500
369
0.306
0.262
1.789
51
807
807
20
87.43
30.7
1.74
28.3
2GU3
12792
12792
0
0
0.056
1
25.5
4.7
98.4
0.451
1.74
1.78
2.44
790
1
3.5
88.6
refinement
REFMAC
5.2.0019
data collection
SBC-Collect
data scaling
SCALEPACK
phasing
HKL-3000
phasing
SHELXD
phasing
MLPHARE
phasing
DM
phasing
SOLVE
phasing
RESOLVE
YpmB protein from Bacillus subtilis
1
N
N
2
N
N
3
N
N
A
GLY
37
A
GLY
12
HELX_P
A
THR
49
A
THR
24
1
1
13
A
LYS
97
A
LYS
72
HELX_P
A
GLY
99
A
GLY
74
5
2
3
A
SER
101
A
SER
76
HELX_P
A
GLU
112
A
GLU
87
1
3
12
metalc
2.189
A
HIS
53
A
NE2
HIS
28
1_555
A
NI
201
B
NI
NI
1_555
metalc
2.149
A
HIS
122
A
NE2
HIS
97
4_466
A
NI
201
B
NI
NI
1_555
metalc
2.252
A
NI
201
B
NI
NI
1_555
A
HOH
219
C
O
HOH
4_466
metalc
2.163
A
NI
201
B
NI
NI
1_555
A
HOH
264
C
O
HOH
1_555
metalc
2.252
A
NI
201
B
NI
NI
1_555
A
HOH
268
C
O
HOH
1_555
metalc
1.774
A
NI
201
B
NI
NI
1_555
A
HOH
295
C
O
HOH
1_555
STRUCTURAL GENOMICS, UNKNOWN FUNCTION
APC1927, structural genomics, PSI, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, UNKNOWN FUNCTION
CAB14154
GB
1
29
2634656
SAMAQKEEGHEAAAAEAKKETDLAHVDQVETFVGKEKYYVVKGTDKKGTALYVWVPADKKAKILSKEAKEGISEDKAAKI
IKDEGLVSKQKEVHLAREGNVLLWEVTYLDKEGQYSLSYVDFTTGKILKNITP
29
161
2GU3
29
161
2634656
A
1
4
136
1
cloning artifact
SER
26
2GU3
A
2634656
GB
1
1
cloning artifact
ASN
27
2GU3
A
2634656
GB
2
1
cloning artifact
ALA
28
2GU3
A
2634656
GB
3
4
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LEU
51
A
LEU
26
A
VAL
61
A
VAL
36
A
LYS
65
A
LYS
40
A
ASP
73
A
ASP
48
A
ALA
78
A
ALA
53
A
PRO
84
A
PRO
59
A
LEU
92
A
LEU
67
A
GLU
95
A
GLU
70
A
LYS
117
A
LYS
92
A
GLU
126
A
GLU
101
A
VAL
129
A
VAL
104
A
LEU
137
A
LEU
112
A
TYR
143
A
TYR
118
A
ASP
149
A
ASP
124
A
ILE
155
A
ILE
130
A
ILE
159
A
ILE
134
BINDING SITE FOR RESIDUE NI A 201
A
NI
201
Software
6
A
HIS
53
A
HIS
28
6
1_555
A
HIS
122
A
HIS
97
6
4_466
A
HOH
219
C
HOH
6
4_466
A
HOH
264
C
HOH
6
1_555
A
HOH
268
C
HOH
6
1_555
A
HOH
295
C
HOH
6
1_555
19
P 21 21 21