0.027153
0.000000
0.000000
0.000000
0.022061
0.000000
0.000000
0.000000
0.017432
0.00000
0.00000
0.00000
Liu, L.
Iwata, K.
Yohda, M.
Miki, K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
36.829
45.328
57.366
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
Ca 2
40.078
CALCIUM ION
non-polymer
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
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
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
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
CA
N
75
N
N
N
76
R
C
N
77
N
C
N
78
N
O
N
79
N
C
N
80
N
S
N
81
N
O
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
H
N
89
N
N
N
90
S
C
N
91
N
C
N
92
N
O
N
93
N
C
N
94
N
C
N
95
N
C
N
96
N
O
N
97
N
N
N
98
N
O
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
H
N
109
N
N
N
110
S
C
N
111
N
C
N
112
N
O
N
113
N
C
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
O
N
118
N
O
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
H
N
128
N
N
N
129
N
C
N
130
N
C
N
131
N
O
N
132
N
O
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
O
N
139
N
H
N
140
N
H
N
141
N
N
N
142
S
C
N
143
N
C
N
144
N
O
N
145
S
C
N
146
N
C
N
147
N
C
N
148
N
C
N
149
N
O
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
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
N
N
164
S
C
N
165
N
C
N
166
N
O
N
167
N
C
N
168
N
C
N
169
N
C
N
170
N
C
N
171
N
O
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
H
N
184
N
H
N
185
N
N
N
186
S
C
N
187
N
C
N
188
N
O
N
189
N
C
N
190
N
C
N
191
N
C
N
192
N
C
N
193
N
N
N
194
N
O
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
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
N
N
211
S
C
N
212
N
C
N
213
N
O
N
214
N
C
N
215
N
C
N
216
N
S
N
217
N
C
N
218
N
O
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
Y
235
N
C
Y
236
N
C
Y
237
N
C
Y
238
N
C
Y
239
N
C
Y
240
N
C
N
241
N
O
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
H
N
251
N
H
N
252
N
H
N
253
N
N
N
254
S
C
N
255
N
C
N
256
N
O
N
257
N
C
N
258
N
C
N
259
N
C
N
260
N
O
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
H
N
268
N
H
N
269
N
H
N
270
N
N
N
271
S
C
N
272
N
C
N
273
N
O
N
274
N
C
N
275
N
O
N
276
N
O
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
R
C
N
289
N
O
N
290
N
C
N
291
N
O
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
H
N
299
N
H
N
300
N
H
N
301
N
N
N
302
S
C
N
303
N
C
N
304
N
O
N
305
N
C
Y
306
N
C
Y
307
N
C
Y
308
N
C
Y
309
N
C
Y
310
N
C
Y
311
N
C
N
312
N
O
N
313
N
O
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
H
N
323
N
H
N
324
N
H
N
325
N
N
N
326
S
C
N
327
N
C
N
328
N
O
N
329
N
C
N
330
N
C
N
331
N
C
N
332
N
O
N
333
N
H
N
334
N
H
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
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
sing
N
136
N
sing
N
137
N
doub
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
sing
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
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
sing
N
201
N
sing
N
202
N
sing
N
203
N
doub
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
doub
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
Y
227
N
doub
Y
228
N
sing
Y
229
N
sing
N
230
N
sing
Y
231
N
doub
N
232
N
sing
Y
233
N
doub
N
234
N
sing
Y
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
sing
N
244
N
sing
N
245
N
doub
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
sing
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
doub
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
doub
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
sing
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
doub
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
Y
296
N
doub
Y
297
N
sing
Y
298
N
sing
N
299
N
sing
Y
300
N
doub
N
301
N
sing
Y
302
N
doub
N
303
N
sing
Y
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
sing
N
313
N
sing
N
314
N
sing
N
315
N
doub
N
316
N
sing
N
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
NE
FEBS LETT.
FEBLAL
0165
0014-5793
528
114
118
10.1016/S0014-5793(02)03264-7
12297289
Structural insight into gene duplication, gene fusion and domain swapping in the evolution of PLP-independent amino acid racemases
2002
10.2210/pdb1iu9/pdb
pdb_00001iu9
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
90
1
CCD
2001-02-28
MARRESEARCH
a fixed-exit double crystal monochramator
SINGLE WAVELENGTH
M
x-ray
1
1.000
1.0
BL44B2
SPring-8
1.000
SYNCHROTRON
SPRING-8 BEAMLINE BL44B2
12176.232
aspartate racemase
5.1.1.13
C-terminal domain
1
man
polymer
40.078
CALCIUM ION
1
syn
non-polymer
18.015
water
56
nat
water
no
no
MIEETAKKVKELGFKKAGLLATTGTIVSGVYEKEFSKYGVEIMTPTEDEQKDVMRGIYEGVKAGNLKLGRELLLKTAKIL
EERGAECIIAGCTEVSVVLKQDDLKVPLIDP
MIEETAKKVKELGFKKAGLLATTGTIVSGVYEKEFSKYGVEIMTPTEDEQKDVMRGIYEGVKAGNLKLGRELLLKTAKIL
EERGAECIIAGCTEVSVVLKQDDLKVPLIDP
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
Pyrococcus
Pyrococcus horikoshii
OT3
Escherichia
Escherichia coli
sample
pPH0670E
70601
Pyrococcus horikoshii
511693
Escherichia coli BL21
BL21
PLASMID
pET23c
1
1.97
37.43
VAPOR DIFFUSION, SITTING DROP
6.5
16% Peg8000, 0.10M MES, 0.2M Calcium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.2K
293.2
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_site
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Source and taxonomy
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2003-09-09
1
1
2008-04-27
1
2
2011-07-13
1
3
2023-12-27
1
4
2024-04-03
_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.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_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
iJFL contains entire protein.
PDBJ
Y
PDBJ
2002-02-28
REL
CA
CALCIUM ION
HOH
water
1JFL
C-terminal domain in the intact structure of aspartate racemase from Pyrococcus horikoshii OT3
PDB
experimental model
CA2
1
2
CA
CA
1
A
WAT
1
3
HOH
HOH
214
A
WAT
2
3
HOH
HOH
215
A
WAT
3
3
HOH
HOH
216
A
WAT
4
3
HOH
HOH
217
A
WAT
5
3
HOH
HOH
218
A
WAT
6
3
HOH
HOH
219
A
WAT
7
3
HOH
HOH
220
A
WAT
8
3
HOH
HOH
221
A
WAT
9
3
HOH
HOH
222
A
WAT
10
3
HOH
HOH
223
A
WAT
11
3
HOH
HOH
224
A
WAT
12
3
HOH
HOH
225
A
WAT
13
3
HOH
HOH
226
A
WAT
14
3
HOH
HOH
227
A
WAT
15
3
HOH
HOH
228
A
WAT
16
3
HOH
HOH
229
A
WAT
17
3
HOH
HOH
230
A
WAT
18
3
HOH
HOH
231
A
WAT
19
3
HOH
HOH
232
A
WAT
20
3
HOH
HOH
233
A
WAT
21
3
HOH
HOH
234
A
WAT
22
3
HOH
HOH
235
A
WAT
23
3
HOH
HOH
236
A
WAT
24
3
HOH
HOH
237
A
WAT
25
3
HOH
HOH
238
A
WAT
26
3
HOH
HOH
239
A
WAT
27
3
HOH
HOH
240
A
WAT
28
3
HOH
HOH
241
A
WAT
29
3
HOH
HOH
242
A
WAT
30
3
HOH
HOH
243
A
WAT
31
3
HOH
HOH
244
A
WAT
32
3
HOH
HOH
245
A
WAT
33
3
HOH
HOH
246
A
WAT
34
3
HOH
HOH
247
A
WAT
35
3
HOH
HOH
248
A
WAT
36
3
HOH
HOH
249
A
WAT
37
3
HOH
HOH
250
A
WAT
38
3
HOH
HOH
251
A
WAT
39
3
HOH
HOH
252
A
WAT
40
3
HOH
HOH
253
A
WAT
41
3
HOH
HOH
254
A
WAT
42
3
HOH
HOH
255
A
WAT
43
3
HOH
HOH
256
A
WAT
44
3
HOH
HOH
257
A
WAT
45
3
HOH
HOH
258
A
WAT
46
3
HOH
HOH
259
A
WAT
47
3
HOH
HOH
260
A
WAT
48
3
HOH
HOH
261
A
WAT
49
3
HOH
HOH
262
A
WAT
50
3
HOH
HOH
263
A
WAT
51
3
HOH
HOH
264
A
WAT
52
3
HOH
HOH
265
A
WAT
53
3
HOH
HOH
266
A
WAT
54
3
HOH
HOH
267
A
WAT
55
3
HOH
HOH
268
A
WAT
56
3
HOH
HOH
269
A
MET
103
n
1
MET
103
A
ILE
104
n
2
ILE
104
A
GLU
105
n
3
GLU
105
A
GLU
106
n
4
GLU
106
A
THR
107
n
5
THR
107
A
ALA
108
n
6
ALA
108
A
LYS
109
n
7
LYS
109
A
LYS
110
n
8
LYS
110
A
VAL
111
n
9
VAL
111
A
LYS
112
n
10
LYS
112
A
GLU
113
n
11
GLU
113
A
LEU
114
n
12
LEU
114
A
GLY
115
n
13
GLY
115
A
PHE
116
n
14
PHE
116
A
LYS
117
n
15
LYS
117
A
LYS
118
n
16
LYS
118
A
ALA
119
n
17
ALA
119
A
GLY
120
n
18
GLY
120
A
LEU
121
n
19
LEU
121
A
LEU
122
n
20
LEU
122
A
ALA
123
n
21
ALA
123
A
THR
124
n
22
THR
124
A
THR
125
n
23
THR
125
A
GLY
126
n
24
GLY
126
A
THR
127
n
25
THR
127
A
ILE
128
n
26
ILE
128
A
VAL
129
n
27
VAL
129
A
SER
130
n
28
SER
130
A
GLY
131
n
29
GLY
131
A
VAL
132
n
30
VAL
132
A
TYR
133
n
31
TYR
133
A
GLU
134
n
32
GLU
134
A
LYS
135
n
33
LYS
135
A
GLU
136
n
34
GLU
136
A
PHE
137
n
35
PHE
137
A
SER
138
n
36
SER
138
A
LYS
139
n
37
LYS
139
A
TYR
140
n
38
TYR
140
A
GLY
141
n
39
GLY
141
A
VAL
142
n
40
VAL
142
A
GLU
143
n
41
GLU
143
A
ILE
144
n
42
ILE
144
A
MET
145
n
43
MET
145
A
THR
146
n
44
THR
146
A
PRO
147
n
45
PRO
147
A
THR
148
n
46
THR
148
A
GLU
149
n
47
GLU
149
A
ASP
150
n
48
ASP
150
A
GLU
151
n
49
GLU
151
A
GLN
152
n
50
GLN
152
A
LYS
153
n
51
LYS
153
A
ASP
154
n
52
ASP
154
A
VAL
155
n
53
VAL
155
A
MET
156
n
54
MET
156
A
ARG
157
n
55
ARG
157
A
GLY
158
n
56
GLY
158
A
ILE
159
n
57
ILE
159
A
TYR
160
n
58
TYR
160
A
GLU
161
n
59
GLU
161
A
GLY
162
n
60
GLY
162
A
VAL
163
n
61
VAL
163
A
LYS
164
n
62
LYS
164
A
ALA
165
n
63
ALA
165
A
GLY
166
n
64
GLY
166
A
ASN
167
n
65
ASN
167
A
LEU
168
n
66
LEU
168
A
LYS
169
n
67
LYS
169
A
LEU
170
n
68
LEU
170
A
GLY
171
n
69
GLY
171
A
ARG
172
n
70
ARG
172
A
GLU
173
n
71
GLU
173
A
LEU
174
n
72
LEU
174
A
LEU
175
n
73
LEU
175
A
LEU
176
n
74
LEU
176
A
LYS
177
n
75
LYS
177
A
THR
178
n
76
THR
178
A
ALA
179
n
77
ALA
179
A
LYS
180
n
78
LYS
180
A
ILE
181
n
79
ILE
181
A
LEU
182
n
80
LEU
182
A
GLU
183
n
81
GLU
183
A
GLU
184
n
82
GLU
184
A
ARG
185
n
83
ARG
185
A
GLY
186
n
84
GLY
186
A
ALA
187
n
85
ALA
187
A
GLU
188
n
86
GLU
188
A
CYS
189
n
87
CYS
189
A
ILE
190
n
88
ILE
190
A
ILE
191
n
89
ILE
191
A
ALA
192
n
90
ALA
192
A
GLY
193
n
91
GLY
193
A
CYS
194
n
92
CYS
194
A
THR
195
n
93
THR
195
A
GLU
196
n
94
GLU
196
A
VAL
197
n
95
VAL
197
A
SER
198
n
96
SER
198
A
VAL
199
n
97
VAL
199
A
VAL
200
n
98
VAL
200
A
LEU
201
n
99
LEU
201
A
LYS
202
n
100
LYS
202
A
GLN
203
n
101
GLN
203
A
ASP
204
n
102
ASP
204
A
ASP
205
n
103
ASP
205
A
LEU
206
n
104
LEU
206
A
LYS
207
n
105
LYS
207
A
VAL
208
n
106
VAL
208
A
PRO
209
n
107
PRO
209
A
LEU
210
n
108
LEU
210
A
ILE
211
n
109
ILE
211
A
ASP
212
n
110
ASP
212
A
PRO
213
n
111
PRO
213
A
author_defined_assembly
1
monomeric
A
GLY
115
A
O
GLY
13
3_545
A
CA
1
B
CA
CA
1_555
A
ASP
204
A
OD2
ASP
102
1_555
149.4
A
GLY
115
A
O
GLY
13
3_545
A
CA
1
B
CA
CA
1_555
A
ASP
204
A
OD1
ASP
102
1_555
157.0
A
ASP
204
A
OD2
ASP
102
1_555
A
CA
1
B
CA
CA
1_555
A
ASP
204
A
OD1
ASP
102
1_555
51.8
A
GLY
115
A
O
GLY
13
3_545
A
CA
1
B
CA
CA
1_555
A
HOH
243
C
O
HOH
1_555
77.6
A
ASP
204
A
OD2
ASP
102
1_555
A
CA
1
B
CA
CA
1_555
A
HOH
243
C
O
HOH
1_555
132.3
A
ASP
204
A
OD1
ASP
102
1_555
A
CA
1
B
CA
CA
1_555
A
HOH
243
C
O
HOH
1_555
80.5
A
GLY
115
A
O
GLY
13
3_545
A
CA
1
B
CA
CA
1_555
A
HOH
244
C
O
HOH
1_555
83.7
A
ASP
204
A
OD2
ASP
102
1_555
A
CA
1
B
CA
CA
1_555
A
HOH
244
C
O
HOH
1_555
85.0
A
ASP
204
A
OD1
ASP
102
1_555
A
CA
1
B
CA
CA
1_555
A
HOH
244
C
O
HOH
1_555
92.5
A
HOH
243
C
O
HOH
1_555
A
CA
1
B
CA
CA
1_555
A
HOH
244
C
O
HOH
1_555
97.9
A
GLY
115
A
O
GLY
13
3_545
A
CA
1
B
CA
CA
1_555
A
HOH
245
C
O
HOH
1_555
105.2
A
ASP
204
A
OD2
ASP
102
1_555
A
CA
1
B
CA
CA
1_555
A
HOH
245
C
O
HOH
1_555
89.1
A
ASP
204
A
OD1
ASP
102
1_555
A
CA
1
B
CA
CA
1_555
A
HOH
245
C
O
HOH
1_555
77.7
A
HOH
243
C
O
HOH
1_555
A
CA
1
B
CA
CA
1_555
A
HOH
245
C
O
HOH
1_555
80.3
A
HOH
244
C
O
HOH
1_555
A
CA
1
B
CA
CA
1_555
A
HOH
245
C
O
HOH
1_555
170.2
A
GLY
115
A
O
GLY
13
3_545
A
CA
1
B
CA
CA
1_555
A
HOH
256
C
O
HOH
1_555
75.6
A
ASP
204
A
OD2
ASP
102
1_555
A
CA
1
B
CA
CA
1_555
A
HOH
256
C
O
HOH
1_555
81.7
A
ASP
204
A
OD1
ASP
102
1_555
A
CA
1
B
CA
CA
1_555
A
HOH
256
C
O
HOH
1_555
126.6
A
HOH
243
C
O
HOH
1_555
A
CA
1
B
CA
CA
1_555
A
HOH
256
C
O
HOH
1_555
138.6
A
HOH
244
C
O
HOH
1_555
A
CA
1
B
CA
CA
1_555
A
HOH
256
C
O
HOH
1_555
109.8
A
HOH
245
C
O
HOH
1_555
A
CA
1
B
CA
CA
1_555
A
HOH
256
C
O
HOH
1_555
77.0
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
O
MET
145
A
O
MET
43
A
N
ALA
119
A
N
ALA
17
A
N
GLY
120
A
N
GLY
18
A
O
ILE
191
A
O
ILE
89
A
N
ILE
190
A
N
ILE
88
A
O
ILE
211
A
O
ILE
109
PROTEIN_REP.PARAM
PROTEIN.TOP
WATER_REP.PARAM
WATER.TOP
ION.PARAM
ION.TOP
23.2
1.91
0.00
0.00
-5.71
0.00
3.80
0.267
0.015
0.225
0.225
2.04
50
334
6491
6457
5.2
99.4
RANDOM
1
RESTRAINED
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
C-terminal domain in the intact structure of aspartate racemase from Pyrococcus horikoshii OT3
Engh & Huber
FLAT MODEL
52.7606
0.371495
0.32
0.21
2.04
50
56
907
1
0
850
0.005
1.1
20.9
0.73
1.42
1.50
2.20
2.00
2.27
2.00
3.38
2.50
0.299
0.039
0.232
2.17
60
986
6
5.7
98.3
21.1
2.04
50
1IU9
34260
34023
3.0
3.0
0.108
0.098
1
5.2
5.4
99.3
0.252
2.04
2.15
3.0
837
0.226
1
5.1
96.3
data reduction
MOSFLM
data scaling
SCALA
phasing
AMoRE
refinement
CNS
1.0
data scaling
CCP4
(SCALA)
Crystal structure of the C-terminal domain of aspartate racemase from Pyrococcus horikoshii OT3
1
N
N
2
N
N
3
N
N
A
MET
103
A
MET
1
HELX_P
A
LEU
114
A
LEU
12
1
1
12
A
THR
124
A
THR
22
HELX_P
A
GLY
131
A
GLY
29
1
2
8
A
GLY
131
A
GLY
29
HELX_P
A
LYS
139
A
LYS
37
1
3
9
A
THR
148
A
THR
46
HELX_P
A
GLU
161
A
GLU
59
1
4
14
A
ASN
167
A
ASN
65
HELX_P
A
ARG
185
A
ARG
83
1
5
19
A
CYS
194
A
CYS
92
HELX_P
A
LEU
201
A
LEU
99
1
6
8
A
LYS
202
A
LYS
100
HELX_P
A
LEU
206
A
LEU
104
5
7
5
metalc
2.358
A
CA
1
B
CA
CA
1_555
A
GLY
115
A
O
GLY
13
3_545
metalc
2.377
A
CA
1
B
CA
CA
1_555
A
ASP
204
A
OD2
ASP
102
1_555
metalc
2.624
A
CA
1
B
CA
CA
1_555
A
ASP
204
A
OD1
ASP
102
1_555
metalc
2.259
A
CA
1
B
CA
CA
1_555
A
HOH
243
C
O
HOH
1_555
metalc
2.423
A
CA
1
B
CA
CA
1_555
A
HOH
244
C
O
HOH
1_555
metalc
2.492
A
CA
1
B
CA
CA
1_555
A
HOH
245
C
O
HOH
1_555
metalc
2.509
A
CA
1
B
CA
CA
1_555
A
HOH
256
C
O
HOH
1_555
ISOMERASE
Aspartate racemase, C-terminal domain, ISOMERASE
O58403_PYRHO
UNP
1
103
O58403
MIEETAKKVKELGFKKAGLLATTGTIVSGVYEKEFSKYGVEIMTPTEDEQKDVMRGIYEGVKAGNLKLGRELLLKTAKIL
EERGAECIIAGCTEVSVVLKQDDLKVPLIDP
103
213
1IU9
103
213
O58403
A
1
1
111
4
parallel
parallel
parallel
A
GLU
143
A
GLU
41
A
MET
145
A
MET
43
A
LYS
118
A
LYS
16
A
LEU
122
A
LEU
20
A
ILE
190
A
ILE
88
A
ALA
192
A
ALA
90
A
LEU
210
A
LEU
108
A
ILE
211
A
ILE
109
BINDING SITE FOR RESIDUE CA A 1
A
CA
1
Software
6
A
GLY
115
A
GLY
13
6
3_545
A
ASP
204
A
ASP
102
6
1_555
A
HOH
243
C
HOH
6
1_555
A
HOH
244
C
HOH
6
1_555
A
HOH
245
C
HOH
6
1_555
A
HOH
256
C
HOH
6
1_555
19
P 21 21 21