0.011045
0.000000
0.007867
0.000000
0.027533
0.000000
0.000000
0.000000
0.016911
0.000000
0.000000
0.000000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
125.460
90.000
90.540
36.320
72.600
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
Fe 3
55.845
FE (III) ION
non-polymer
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 Se
196.106
n
SELENOMETHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
O4 P -3
94.971
PHOSPHATE ION
non-polymer
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 predicted HD superfamily hydrolase involved in NAD metabolism (NP_347894.1) from Clostridium acetobutylicum at 1.50 A resolution
10.2210/pdb3ccg/pdb
pdb_00003ccg
100
1
Flat mirror (vertical focusing)
CCD
2008-02-01
MARMOSAIC 325 mm CCD
Single crystal Si(111) bent (horizontal focusing)
MAD
M
x-ray
1
0.91837
1.0
0.97922
1.0
0.97874
1.0
BL11-1
SSRL
0.91837, 0.97922, 0.97874
SYNCHROTRON
SSRL BEAMLINE BL11-1
21759.070
HD superfamily hydrolase
1
man
polymer
55.845
FE (III) ION
2
syn
non-polymer
94.971
PHOSPHATE ION
1
syn
non-polymer
18.015
water
198
nat
water
no
yes
G(MSE)WSYDKITDYL(MSE)NNLGEKRYKHSLGV(MSE)DTAVRLAGIYNEDTEKARIAGLVHDCAKKLPGEKIIEICT
NEGYELGDEDIRNSYLLHGLAGRILAKKVIGIDDEDVLNAIEFHTTGRPN(MSE)SLLEKIIYIADYIEPGREFKGVDEL
RKAADEDLNKALL(MSE)SFDNTIKFVIDKGGFLHHNTIEARNYLISRKG
GMWSYDKITDYLMNNLGEKRYKHSLGVMDTAVRLAGIYNEDTEKARIAGLVHDCAKKLPGEKIIEICTNEGYELGDEDIR
NSYLLHGLAGRILAKKVIGIDDEDVLNAIEFHTTGRPNMSLLEKIIYIADYIEPGREFKGVDELRKAADEDLNKALLMSF
DNTIKFVIDKGGFLHHNTIEARNYLISRKG
A
367850
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
Clostridium
Clostridium acetobutylicum
DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787
Escherichia
sample
NP_347894.1, CA_C1263
272562
Clostridium acetobutylicum ATCC 824
562
Escherichia coli
HK100
Plasmid
SpeedET
1
2.23
44.95
VAPOR DIFFUSION, SITTING DROP
5.9
NANODROP, 0.2M Mg formate, 20.0% PEG 3350, 0.001M Spermine tetra-HCl, No Buffer pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
277
Joint Center for Structural Genomics
JCSG
PSI, Protein Structure Initiative
software
software
struct_conn
database_2
pdbx_struct_conn_angle
struct_conn
struct_conn_type
struct_ref_seq_dif
struct_site
repository
Initial release
Advisory
Version format compliance
Refinement description
Data collection
Derived calculations
Refinement description
Database references
Derived calculations
1
0
2008-03-11
1
1
2011-07-13
1
2
2017-10-25
1
3
2019-07-24
1
4
2023-02-01
_software.classification
_software.name
_software.classification
_software.contact_author
_software.contact_author_email
_software.language
_software.location
_software.name
_software.type
_software.version
_struct_conn.pdbx_leaving_atom_flag
_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.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.value
_struct_conn.conn_type_id
_struct_conn.id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr2_label_alt_id
_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
_struct_conn_type.id
_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
2008-02-25
REL
REL
FE
FE (III) ION
PO4
PHOSPHATE ION
HOH
water
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG
MGSDKIHHHHHH. THE TAG WAS REMOVED WITH TEV PROTEASE
LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
FE
1
2
FE
FE
190
A
FE
2
2
FE
FE
191
A
PO4
3
3
PO4
PO4
192
A
HOH
4
4
HOH
HOH
193
A
HOH
5
4
HOH
HOH
194
A
HOH
6
4
HOH
HOH
195
A
HOH
7
4
HOH
HOH
196
A
HOH
8
4
HOH
HOH
197
A
HOH
9
4
HOH
HOH
198
A
HOH
10
4
HOH
HOH
199
A
HOH
11
4
HOH
HOH
200
A
HOH
12
4
HOH
HOH
201
A
HOH
13
4
HOH
HOH
202
A
HOH
14
4
HOH
HOH
203
A
HOH
15
4
HOH
HOH
204
A
HOH
16
4
HOH
HOH
205
A
HOH
17
4
HOH
HOH
206
A
HOH
18
4
HOH
HOH
207
A
HOH
19
4
HOH
HOH
208
A
HOH
20
4
HOH
HOH
209
A
HOH
21
4
HOH
HOH
210
A
HOH
22
4
HOH
HOH
211
A
HOH
23
4
HOH
HOH
212
A
HOH
24
4
HOH
HOH
213
A
HOH
25
4
HOH
HOH
214
A
HOH
26
4
HOH
HOH
215
A
HOH
27
4
HOH
HOH
216
A
HOH
28
4
HOH
HOH
217
A
HOH
29
4
HOH
HOH
218
A
HOH
30
4
HOH
HOH
219
A
HOH
31
4
HOH
HOH
220
A
HOH
32
4
HOH
HOH
221
A
HOH
33
4
HOH
HOH
222
A
HOH
34
4
HOH
HOH
223
A
HOH
35
4
HOH
HOH
224
A
HOH
36
4
HOH
HOH
225
A
HOH
37
4
HOH
HOH
226
A
HOH
38
4
HOH
HOH
227
A
HOH
39
4
HOH
HOH
228
A
HOH
40
4
HOH
HOH
229
A
HOH
41
4
HOH
HOH
230
A
HOH
42
4
HOH
HOH
231
A
HOH
43
4
HOH
HOH
232
A
HOH
44
4
HOH
HOH
233
A
HOH
45
4
HOH
HOH
234
A
HOH
46
4
HOH
HOH
235
A
HOH
47
4
HOH
HOH
236
A
HOH
48
4
HOH
HOH
237
A
HOH
49
4
HOH
HOH
238
A
HOH
50
4
HOH
HOH
239
A
HOH
51
4
HOH
HOH
240
A
HOH
52
4
HOH
HOH
241
A
HOH
53
4
HOH
HOH
242
A
HOH
54
4
HOH
HOH
243
A
HOH
55
4
HOH
HOH
244
A
HOH
56
4
HOH
HOH
245
A
HOH
57
4
HOH
HOH
246
A
HOH
58
4
HOH
HOH
247
A
HOH
59
4
HOH
HOH
248
A
HOH
60
4
HOH
HOH
249
A
HOH
61
4
HOH
HOH
250
A
HOH
62
4
HOH
HOH
251
A
HOH
63
4
HOH
HOH
252
A
HOH
64
4
HOH
HOH
253
A
HOH
65
4
HOH
HOH
254
A
HOH
66
4
HOH
HOH
255
A
HOH
67
4
HOH
HOH
256
A
HOH
68
4
HOH
HOH
257
A
HOH
69
4
HOH
HOH
258
A
HOH
70
4
HOH
HOH
259
A
HOH
71
4
HOH
HOH
260
A
HOH
72
4
HOH
HOH
261
A
HOH
73
4
HOH
HOH
262
A
HOH
74
4
HOH
HOH
263
A
HOH
75
4
HOH
HOH
264
A
HOH
76
4
HOH
HOH
265
A
HOH
77
4
HOH
HOH
266
A
HOH
78
4
HOH
HOH
267
A
HOH
79
4
HOH
HOH
268
A
HOH
80
4
HOH
HOH
269
A
HOH
81
4
HOH
HOH
270
A
HOH
82
4
HOH
HOH
271
A
HOH
83
4
HOH
HOH
272
A
HOH
84
4
HOH
HOH
273
A
HOH
85
4
HOH
HOH
274
A
HOH
86
4
HOH
HOH
275
A
HOH
87
4
HOH
HOH
276
A
HOH
88
4
HOH
HOH
277
A
HOH
89
4
HOH
HOH
278
A
HOH
90
4
HOH
HOH
279
A
HOH
91
4
HOH
HOH
280
A
HOH
92
4
HOH
HOH
281
A
HOH
93
4
HOH
HOH
282
A
HOH
94
4
HOH
HOH
283
A
HOH
95
4
HOH
HOH
284
A
HOH
96
4
HOH
HOH
285
A
HOH
97
4
HOH
HOH
286
A
HOH
98
4
HOH
HOH
287
A
HOH
99
4
HOH
HOH
288
A
HOH
100
4
HOH
HOH
289
A
HOH
101
4
HOH
HOH
290
A
HOH
102
4
HOH
HOH
291
A
HOH
103
4
HOH
HOH
292
A
HOH
104
4
HOH
HOH
293
A
HOH
105
4
HOH
HOH
294
A
HOH
106
4
HOH
HOH
295
A
HOH
107
4
HOH
HOH
296
A
HOH
108
4
HOH
HOH
297
A
HOH
109
4
HOH
HOH
298
A
HOH
110
4
HOH
HOH
299
A
HOH
111
4
HOH
HOH
300
A
HOH
112
4
HOH
HOH
301
A
HOH
113
4
HOH
HOH
302
A
HOH
114
4
HOH
HOH
303
A
HOH
115
4
HOH
HOH
304
A
HOH
116
4
HOH
HOH
305
A
HOH
117
4
HOH
HOH
306
A
HOH
118
4
HOH
HOH
307
A
HOH
119
4
HOH
HOH
308
A
HOH
120
4
HOH
HOH
309
A
HOH
121
4
HOH
HOH
310
A
HOH
122
4
HOH
HOH
311
A
HOH
123
4
HOH
HOH
312
A
HOH
124
4
HOH
HOH
313
A
HOH
125
4
HOH
HOH
314
A
HOH
126
4
HOH
HOH
315
A
HOH
127
4
HOH
HOH
316
A
HOH
128
4
HOH
HOH
317
A
HOH
129
4
HOH
HOH
318
A
HOH
130
4
HOH
HOH
319
A
HOH
131
4
HOH
HOH
320
A
HOH
132
4
HOH
HOH
321
A
HOH
133
4
HOH
HOH
322
A
HOH
134
4
HOH
HOH
323
A
HOH
135
4
HOH
HOH
324
A
HOH
136
4
HOH
HOH
325
A
HOH
137
4
HOH
HOH
326
A
HOH
138
4
HOH
HOH
327
A
HOH
139
4
HOH
HOH
328
A
HOH
140
4
HOH
HOH
329
A
HOH
141
4
HOH
HOH
330
A
HOH
142
4
HOH
HOH
331
A
HOH
143
4
HOH
HOH
332
A
HOH
144
4
HOH
HOH
333
A
HOH
145
4
HOH
HOH
334
A
HOH
146
4
HOH
HOH
335
A
HOH
147
4
HOH
HOH
336
A
HOH
148
4
HOH
HOH
337
A
HOH
149
4
HOH
HOH
338
A
HOH
150
4
HOH
HOH
339
A
HOH
151
4
HOH
HOH
340
A
HOH
152
4
HOH
HOH
341
A
HOH
153
4
HOH
HOH
342
A
HOH
154
4
HOH
HOH
343
A
HOH
155
4
HOH
HOH
344
A
HOH
156
4
HOH
HOH
345
A
HOH
157
4
HOH
HOH
346
A
HOH
158
4
HOH
HOH
347
A
HOH
159
4
HOH
HOH
348
A
HOH
160
4
HOH
HOH
349
A
HOH
161
4
HOH
HOH
350
A
HOH
162
4
HOH
HOH
351
A
HOH
163
4
HOH
HOH
352
A
HOH
164
4
HOH
HOH
353
A
HOH
165
4
HOH
HOH
354
A
HOH
166
4
HOH
HOH
355
A
HOH
167
4
HOH
HOH
356
A
HOH
168
4
HOH
HOH
357
A
HOH
169
4
HOH
HOH
358
A
HOH
170
4
HOH
HOH
359
A
HOH
171
4
HOH
HOH
360
A
HOH
172
4
HOH
HOH
361
A
HOH
173
4
HOH
HOH
362
A
HOH
174
4
HOH
HOH
363
A
HOH
175
4
HOH
HOH
364
A
HOH
176
4
HOH
HOH
365
A
HOH
177
4
HOH
HOH
366
A
HOH
178
4
HOH
HOH
367
A
HOH
179
4
HOH
HOH
368
A
HOH
180
4
HOH
HOH
369
A
HOH
181
4
HOH
HOH
370
A
HOH
182
4
HOH
HOH
371
A
HOH
183
4
HOH
HOH
372
A
HOH
184
4
HOH
HOH
373
A
HOH
185
4
HOH
HOH
374
A
HOH
186
4
HOH
HOH
375
A
HOH
187
4
HOH
HOH
376
A
HOH
188
4
HOH
HOH
377
A
HOH
189
4
HOH
HOH
378
A
HOH
190
4
HOH
HOH
379
A
HOH
191
4
HOH
HOH
380
A
HOH
192
4
HOH
HOH
381
A
HOH
193
4
HOH
HOH
382
A
HOH
194
4
HOH
HOH
383
A
HOH
195
4
HOH
HOH
384
A
HOH
196
4
HOH
HOH
385
A
HOH
197
4
HOH
HOH
386
A
HOH
198
4
HOH
HOH
387
A
HOH
199
4
HOH
HOH
388
A
HOH
200
4
HOH
HOH
389
A
HOH
201
4
HOH
HOH
390
A
GLY
0
n
1
GLY
0
A
MSE
1
n
2
MSE
1
A
TRP
2
n
3
TRP
2
A
SER
3
n
4
SER
3
A
TYR
4
n
5
TYR
4
A
ASP
5
n
6
ASP
5
A
LYS
6
n
7
LYS
6
A
ILE
7
n
8
ILE
7
A
THR
8
n
9
THR
8
A
ASP
9
n
10
ASP
9
A
TYR
10
n
11
TYR
10
A
LEU
11
n
12
LEU
11
A
MSE
12
n
13
MSE
12
A
ASN
13
n
14
ASN
13
A
ASN
14
n
15
ASN
14
A
LEU
15
n
16
LEU
15
A
GLY
16
n
17
GLY
16
A
GLU
17
n
18
GLU
17
A
LYS
18
n
19
LYS
18
A
ARG
19
n
20
ARG
19
A
TYR
20
n
21
TYR
20
A
LYS
21
n
22
LYS
21
A
HIS
22
n
23
HIS
22
A
SER
23
n
24
SER
23
A
LEU
24
n
25
LEU
24
A
GLY
25
n
26
GLY
25
A
VAL
26
n
27
VAL
26
A
MSE
27
n
28
MSE
27
A
ASP
28
n
29
ASP
28
A
THR
29
n
30
THR
29
A
ALA
30
n
31
ALA
30
A
VAL
31
n
32
VAL
31
A
ARG
32
n
33
ARG
32
A
LEU
33
n
34
LEU
33
A
ALA
34
n
35
ALA
34
A
GLY
35
n
36
GLY
35
A
ILE
36
n
37
ILE
36
A
TYR
37
n
38
TYR
37
A
ASN
38
n
39
ASN
38
A
GLU
39
n
40
GLU
39
A
ASP
40
n
41
ASP
40
A
THR
41
n
42
THR
41
A
GLU
42
n
43
GLU
42
A
LYS
43
n
44
LYS
43
A
ALA
44
n
45
ALA
44
A
ARG
45
n
46
ARG
45
A
ILE
46
n
47
ILE
46
A
ALA
47
n
48
ALA
47
A
GLY
48
n
49
GLY
48
A
LEU
49
n
50
LEU
49
A
VAL
50
n
51
VAL
50
A
HIS
51
n
52
HIS
51
A
ASP
52
n
53
ASP
52
A
CYS
53
n
54
CYS
53
A
ALA
54
n
55
ALA
54
A
LYS
55
n
56
LYS
55
A
LYS
56
n
57
LYS
56
A
LEU
57
n
58
LEU
57
A
PRO
58
n
59
PRO
58
A
GLY
59
n
60
GLY
59
A
GLU
60
n
61
GLU
60
A
LYS
61
n
62
LYS
61
A
ILE
62
n
63
ILE
62
A
ILE
63
n
64
ILE
63
A
GLU
64
n
65
GLU
64
A
ILE
65
n
66
ILE
65
A
CYS
66
n
67
CYS
66
A
THR
67
n
68
THR
67
A
ASN
68
n
69
ASN
68
A
GLU
69
n
70
GLU
69
A
GLY
70
n
71
GLY
70
A
TYR
71
n
72
TYR
71
A
GLU
72
n
73
GLU
72
A
LEU
73
n
74
LEU
73
A
GLY
74
n
75
GLY
74
A
ASP
75
n
76
ASP
75
A
GLU
76
n
77
GLU
76
A
ASP
77
n
78
ASP
77
A
ILE
78
n
79
ILE
78
A
ARG
79
n
80
ARG
79
A
ASN
80
n
81
ASN
80
A
SER
81
n
82
SER
81
A
TYR
82
n
83
TYR
82
A
LEU
83
n
84
LEU
83
A
LEU
84
n
85
LEU
84
A
HIS
85
n
86
HIS
85
A
GLY
86
n
87
GLY
86
A
LEU
87
n
88
LEU
87
A
ALA
88
n
89
ALA
88
A
GLY
89
n
90
GLY
89
A
ARG
90
n
91
ARG
90
A
ILE
91
n
92
ILE
91
A
LEU
92
n
93
LEU
92
A
ALA
93
n
94
ALA
93
A
LYS
94
n
95
LYS
94
A
LYS
95
n
96
LYS
95
A
VAL
96
n
97
VAL
96
A
ILE
97
n
98
ILE
97
A
GLY
98
n
99
GLY
98
A
ILE
99
n
100
ILE
99
A
ASP
100
n
101
ASP
100
A
ASP
101
n
102
ASP
101
A
GLU
102
n
103
GLU
102
A
ASP
103
n
104
ASP
103
A
VAL
104
n
105
VAL
104
A
LEU
105
n
106
LEU
105
A
ASN
106
n
107
ASN
106
A
ALA
107
n
108
ALA
107
A
ILE
108
n
109
ILE
108
A
GLU
109
n
110
GLU
109
A
PHE
110
n
111
PHE
110
A
HIS
111
n
112
HIS
111
A
THR
112
n
113
THR
112
A
THR
113
n
114
THR
113
A
GLY
114
n
115
GLY
114
A
ARG
115
n
116
ARG
115
A
PRO
116
n
117
PRO
116
A
ASN
117
n
118
ASN
117
A
MSE
118
n
119
MSE
118
A
SER
119
n
120
SER
119
A
LEU
120
n
121
LEU
120
A
LEU
121
n
122
LEU
121
A
GLU
122
n
123
GLU
122
A
LYS
123
n
124
LYS
123
A
ILE
124
n
125
ILE
124
A
ILE
125
n
126
ILE
125
A
TYR
126
n
127
TYR
126
A
ILE
127
n
128
ILE
127
A
ALA
128
n
129
ALA
128
A
ASP
129
n
130
ASP
129
A
TYR
130
n
131
TYR
130
A
ILE
131
n
132
ILE
131
A
GLU
132
n
133
GLU
132
A
PRO
133
n
134
PRO
133
A
GLY
134
n
135
GLY
134
A
ARG
135
n
136
ARG
135
A
GLU
136
n
137
GLU
136
A
PHE
137
n
138
PHE
137
A
LYS
138
n
139
LYS
138
A
GLY
139
n
140
GLY
139
A
VAL
140
n
141
VAL
140
A
ASP
141
n
142
ASP
141
A
GLU
142
n
143
GLU
142
A
LEU
143
n
144
LEU
143
A
ARG
144
n
145
ARG
144
A
LYS
145
n
146
LYS
145
A
ALA
146
n
147
ALA
146
A
ALA
147
n
148
ALA
147
A
ASP
148
n
149
ASP
148
A
GLU
149
n
150
GLU
149
A
ASP
150
n
151
ASP
150
A
LEU
151
n
152
LEU
151
A
ASN
152
n
153
ASN
152
A
LYS
153
n
154
LYS
153
A
ALA
154
n
155
ALA
154
A
LEU
155
n
156
LEU
155
A
LEU
156
n
157
LEU
156
A
MSE
157
n
158
MSE
157
A
SER
158
n
159
SER
158
A
PHE
159
n
160
PHE
159
A
ASP
160
n
161
ASP
160
A
ASN
161
n
162
ASN
161
A
THR
162
n
163
THR
162
A
ILE
163
n
164
ILE
163
A
LYS
164
n
165
LYS
164
A
PHE
165
n
166
PHE
165
A
VAL
166
n
167
VAL
166
A
ILE
167
n
168
ILE
167
A
ASP
168
n
169
ASP
168
A
LYS
169
n
170
LYS
169
A
GLY
170
n
171
GLY
170
A
GLY
171
n
172
GLY
171
A
PHE
172
n
173
PHE
172
A
LEU
173
n
174
LEU
173
A
HIS
174
n
175
HIS
174
A
HIS
175
n
176
HIS
175
A
ASN
176
n
177
ASN
176
A
THR
177
n
178
THR
177
A
ILE
178
n
179
ILE
178
A
GLU
179
n
180
GLU
179
A
ALA
180
n
181
ALA
180
A
ARG
181
n
182
ARG
181
A
ASN
182
n
183
ASN
182
A
TYR
183
n
184
TYR
183
A
LEU
184
n
185
LEU
184
A
ILE
185
n
186
ILE
185
A
SER
186
n
187
SER
186
A
ARG
187
n
188
ARG
187
A
LYS
188
n
189
LYS
188
A
n
190
189
A
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
0.0000
refined
0.0000
0.0000
0.0000
X-RAY DIFFRACTION
A
0
A
1
A
188
A
189
X-RAY DIFFRACTION
1
software_defined_assembly
PISA
2
dimeric
1390
-7.2
17530
A
HIS
22
A
NE2
HIS
23
1_555
A
FE
191
C
FE
FE
1_555
A
HIS
51
A
NE2
HIS
52
1_555
97.5
A
HIS
22
A
NE2
HIS
23
1_555
A
FE
191
C
FE
FE
1_555
A
ASP
52
A
OD2
ASP
53
1_555
90.1
A
HIS
51
A
NE2
HIS
52
1_555
A
FE
191
C
FE
FE
1_555
A
ASP
52
A
OD2
ASP
53
1_555
82.6
A
HIS
22
A
NE2
HIS
23
1_555
A
FE
191
C
FE
FE
1_555
A
ASP
129
A
OD1
ASP
130
1_555
77.5
A
HIS
51
A
NE2
HIS
52
1_555
A
FE
191
C
FE
FE
1_555
A
ASP
129
A
OD1
ASP
130
1_555
96.6
A
ASP
52
A
OD2
ASP
53
1_555
A
FE
191
C
FE
FE
1_555
A
ASP
129
A
OD1
ASP
130
1_555
167.4
A
HIS
22
A
NE2
HIS
23
1_555
A
FE
191
C
FE
FE
1_555
A
PO4
192
D
O4
PO4
1_555
82.2
A
HIS
51
A
NE2
HIS
52
1_555
A
FE
191
C
FE
FE
1_555
A
PO4
192
D
O4
PO4
1_555
173.4
A
ASP
52
A
OD2
ASP
53
1_555
A
FE
191
C
FE
FE
1_555
A
PO4
192
D
O4
PO4
1_555
90.8
A
ASP
129
A
OD1
ASP
130
1_555
A
FE
191
C
FE
FE
1_555
A
PO4
192
D
O4
PO4
1_555
89.8
A
HIS
22
A
NE2
HIS
23
1_555
A
FE
191
C
FE
FE
1_555
A
HOH
195
E
O
HOH
1_555
175.0
A
HIS
51
A
NE2
HIS
52
1_555
A
FE
191
C
FE
FE
1_555
A
HOH
195
E
O
HOH
1_555
83.9
A
ASP
52
A
OD2
ASP
53
1_555
A
FE
191
C
FE
FE
1_555
A
HOH
195
E
O
HOH
1_555
94.8
A
ASP
129
A
OD1
ASP
130
1_555
A
FE
191
C
FE
FE
1_555
A
HOH
195
E
O
HOH
1_555
97.7
A
PO4
192
D
O4
PO4
1_555
A
FE
191
C
FE
FE
1_555
A
HOH
195
E
O
HOH
1_555
97.0
A
ASP
52
A
OD1
ASP
53
1_555
A
FE
190
B
FE
FE
1_555
A
HIS
85
A
NE2
HIS
86
1_555
86.7
A
ASP
52
A
OD1
ASP
53
1_555
A
FE
190
B
FE
FE
1_555
A
HIS
111
A
NE2
HIS
112
1_555
90.7
A
HIS
85
A
NE2
HIS
86
1_555
A
FE
190
B
FE
FE
1_555
A
HIS
111
A
NE2
HIS
112
1_555
93.6
A
ASP
52
A
OD1
ASP
53
1_555
A
FE
190
B
FE
FE
1_555
A
PO4
192
D
O1
PO4
1_555
92.2
A
HIS
85
A
NE2
HIS
86
1_555
A
FE
190
B
FE
FE
1_555
A
PO4
192
D
O1
PO4
1_555
93.1
A
HIS
111
A
NE2
HIS
112
1_555
A
FE
190
B
FE
FE
1_555
A
PO4
192
D
O1
PO4
1_555
172.9
A
ASP
52
A
OD1
ASP
53
1_555
A
FE
190
B
FE
FE
1_555
A
HOH
195
E
O
HOH
1_555
89.0
A
HIS
85
A
NE2
HIS
86
1_555
A
FE
190
B
FE
FE
1_555
A
HOH
195
E
O
HOH
1_555
175.6
A
HIS
111
A
NE2
HIS
112
1_555
A
FE
190
B
FE
FE
1_555
A
HOH
195
E
O
HOH
1_555
87.5
A
PO4
192
D
O1
PO4
1_555
A
FE
190
B
FE
FE
1_555
A
HOH
195
E
O
HOH
1_555
86.1
A
ASP
52
A
OD1
ASP
53
1_555
A
FE
190
B
FE
FE
1_555
A
HOH
199
E
O
HOH
1_555
176.6
A
HIS
85
A
NE2
HIS
86
1_555
A
FE
190
B
FE
FE
1_555
A
HOH
199
E
O
HOH
1_555
94.4
A
HIS
111
A
NE2
HIS
112
1_555
A
FE
190
B
FE
FE
1_555
A
HOH
199
E
O
HOH
1_555
92.4
A
PO4
192
D
O1
PO4
1_555
A
FE
190
B
FE
FE
1_555
A
HOH
199
E
O
HOH
1_555
84.5
A
HOH
195
E
O
HOH
1_555
A
FE
190
B
FE
FE
1_555
A
HOH
199
E
O
HOH
1_555
89.8
A
MSE
1
SELENOMETHIONINE
A
MSE
2
MET
A
MSE
12
SELENOMETHIONINE
A
MSE
13
MET
A
MSE
27
SELENOMETHIONINE
A
MSE
28
MET
A
MSE
118
SELENOMETHIONINE
A
MSE
119
MET
A
MSE
157
SELENOMETHIONINE
A
MSE
158
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
2_555
-x,y,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
1
A
CD
GLU
17
A
CD
GLU
18
1
Y
1
A
OE1
GLU
17
A
OE1
GLU
18
1
Y
1
A
OE2
GLU
17
A
OE2
GLU
18
1
Y
1
A
CD
LYS
18
A
CD
LYS
19
1
Y
1
A
CE
LYS
18
A
CE
LYS
19
1
Y
1
A
NZ
LYS
18
A
NZ
LYS
19
1
Y
1
A
CD
LYS
21
A
CD
LYS
22
1
Y
1
A
CE
LYS
21
A
CE
LYS
22
1
Y
1
A
NZ
LYS
21
A
NZ
LYS
22
1
Y
1
A
CG
GLU
72
A
CG
GLU
73
1
Y
1
A
CD
GLU
72
A
CD
GLU
73
1
Y
1
A
OE1
GLU
72
A
OE1
GLU
73
1
Y
1
A
OE2
GLU
72
A
OE2
GLU
73
1
Y
1
A
CD
GLU
76
A
CD
GLU
77
1
Y
1
A
OE1
GLU
76
A
OE1
GLU
77
1
Y
1
A
OE2
GLU
76
A
OE2
GLU
77
1
Y
1
A
CG
ASN
80
A
CG
ASN
81
1
Y
1
A
OD1
ASN
80
A
OD1
ASN
81
1
Y
1
A
ND2
ASN
80
A
ND2
ASN
81
1
Y
1
A
N
LEU
84
A
N
LEU
85
1
Y
1
A
CD
GLU
102
A
CD
GLU
103
1
Y
1
A
OE1
GLU
102
A
OE1
GLU
103
1
Y
1
A
OE2
GLU
102
A
OE2
GLU
103
1
Y
1
A
CE
LYS
138
A
CE
LYS
139
1
Y
1
A
NZ
LYS
138
A
NZ
LYS
139
1
Y
1
A
CG
ASP
141
A
CG
ASP
142
1
Y
1
A
OD1
ASP
141
A
OD1
ASP
142
1
Y
1
A
OD2
ASP
141
A
OD2
ASP
142
1
Y
1
A
CE
LYS
145
A
CE
LYS
146
1
Y
1
A
NZ
LYS
145
A
NZ
LYS
146
1
Y
1
A
NZ
LYS
153
A
NZ
LYS
154
1
Y
1
A
CZ
ARG
187
A
CZ
ARG
188
1
Y
1
A
NH1
ARG
187
A
NH1
ARG
188
1
Y
1
A
NH2
ARG
187
A
NH2
ARG
188
1
Y
1
A
GLY
189
A
GLY
190
1
Y
1
A
A
OH
OE2
TYR
GLU
4
42
1.83
B
1
A
A
O
O
HOH
HOH
201
261
1.89
1
A
A
OE2
O
GLU
HOH
64
201
2.03
A
1
A
A
O
O
HOH
HOH
201
245
2.17
1
A
A
CG
CD1
TYR
TYR
82
82
-0.086
0.013
1.387
1.301
B
B
N
1
A
A
O3
O
PO4
HOH
192
201
2.03
1_555
4_555
1
A
ASN
80
-115.85
74.65
15.356
-0.750
0.000
-1.000
0.290
0.000
-0.700
0.964
0.945
1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
3. 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
TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL
S-MET INCORPORATION.
4. IRON HAS BEEN MODELED IN THE PUTATIVE ACTIVE SITE BASED ON AN X-RAY
FLUORESCENCE SCAN FOR METAL, ANOMALOUS DIFFERENCE FOURIERS, AND
COORDINATION GEOMETRY.
5. PHOSPHATE IS MODELED BASED ON ELECTRON DENSITY AND PROPOSED FUNCTION.
0.217
0.180
0.182
1.500
25.872
1560
30979
5.000
99.560
1.381
0.053
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
0.00
MAD
0.079
0.082
0.800
0.800
1.200
MAXIMUM LIKELIHOOD WITH PHASES
MASK
1.500
25.872
198
1677
7
0
1472
0.017
0.022
1639
0.001
0.020
1103
1.563
1.965
2227
1.065
3.000
2694
3.972
5.000
214
33.877
24.156
77
11.479
15.000
295
13.723
15.000
11
0.078
0.200
241
0.007
0.020
1897
0.002
0.020
341
1.826
3.000
1012
0.527
3.000
417
2.848
5.000
1634
4.390
8.000
627
6.330
11.000
593
0.284
0.231
1.539
109
2152
2261
20
98.560
17.062
1.50
25.872
3CCG
30979
-3.00
0.038
1
11.530
98.300
0.362
1.50
1.55
2.1
10409
5469
1
96.70
0.271
1.55
1.62
2.7
12822
6692
1
97.80
0.199
1.62
1.69
3.6
10764
5622
1
98.30
0.158
1.69
1.78
4.5
11514
6010
1
98.70
0.116
1.78
1.89
6.4
11230
5863
1
98.80
0.074
1.89
2.04
9.4
11789
6153
1
99.00
0.047
2.04
2.24
14.4
11229
5835
1
99.00
0.036
2.24
2.56
18.4
11466
5953
1
99.00
0.028
2.56
3.23
23.6
11670
6030
1
98.60
0.022
3.23
25.872
30.1
11506
5914
1
97.10
refinement
Murshudov, G.N.
ccp4@dl.ac.uk
Fortran_77
http://www.ccp4.ac.uk/main.html
REFMAC
program
5.4.0067
refinement
P.D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
phasing
George Sheldrick
gsheldr@shelx.uni-ac.gwdg.de
Fortran_77
http://shelx.uni-ac.gwdg.de/SHELX/
SHELX
package
model building
D.C. & J.S. Richardson lab
molprobity@kinemage.biochem.duke.edu
http://kinemage.biochem.duke.edu/molprobity/
MolProbity
package
3beta29
data scaling
Wolfgang Kabsch
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/xscale_program.html
XSCALE
package
data extraction
PDB
sw-help@rcsb.rutgers.edu
July 2, 2007
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
3.000
data collection
MAR345
CCD
data reduction
XDS
phasing
SHELXD
phasing
autoSHARP
Crystal structure of predicted HD superfamily hydrolase involved in NAD metabolism (NP_347894.1) from Clostridium acetobutylicum at 1.50 A resolution
1
N
N
2
N
N
2
N
N
3
N
N
4
N
N
A
SER
3
A
SER
4
HELX_P
A
ASN
38
A
ASN
39
1
1
36
A
ASP
40
A
ASP
41
HELX_P
A
HIS
51
A
HIS
52
1
2
12
A
PRO
58
A
PRO
59
HELX_P
A
GLU
69
A
GLU
70
1
3
12
A
GLY
74
A
GLY
75
HELX_P
A
ARG
79
A
ARG
80
1
4
6
A
LEU
84
A
LEU
85
HELX_P
A
VAL
96
A
VAL
97
1
5
13
A
ASP
101
A
ASP
102
HELX_P
A
PHE
110
A
PHE
111
1
6
10
A
SER
119
A
SER
120
HELX_P
A
GLU
132
A
GLU
133
1
7
14
A
GLY
139
A
GLY
140
HELX_P
A
ASP
150
A
ASP
151
1
8
12
A
ASP
150
A
ASP
151
HELX_P
A
GLY
170
A
GLY
171
1
9
21
A
HIS
174
A
HIS
175
HELX_P
A
LYS
188
A
LYS
189
1
10
15
covale
1.330
both
A
GLY
0
A
C
GLY
1
1_555
A
MSE
1
A
N
MSE
2
1_555
covale
1.328
both
A
MSE
1
A
C
MSE
2
1_555
A
TRP
2
A
N
TRP
3
1_555
covale
1.327
both
A
A
LEU
11
A
C
LEU
12
1_555
A
MSE
12
A
N
MSE
13
1_555
covale
1.327
both
B
A
LEU
11
A
C
LEU
12
1_555
A
MSE
12
A
N
MSE
13
1_555
covale
1.327
both
A
A
A
MSE
12
A
C
MSE
13
1_555
A
ASN
13
A
N
ASN
14
1_555
covale
1.327
both
B
B
A
MSE
12
A
C
MSE
13
1_555
A
ASN
13
A
N
ASN
14
1_555
covale
1.320
both
A
VAL
26
A
C
VAL
27
1_555
A
MSE
27
A
N
MSE
28
1_555
covale
1.325
both
A
MSE
27
A
C
MSE
28
1_555
A
ASP
28
A
N
ASP
29
1_555
covale
1.317
both
A
ASN
117
A
C
ASN
118
1_555
A
MSE
118
A
N
MSE
119
1_555
covale
1.322
both
A
MSE
118
A
C
MSE
119
1_555
A
SER
119
A
N
SER
120
1_555
covale
1.328
both
A
A
LEU
156
A
C
LEU
157
1_555
A
MSE
157
A
N
MSE
158
1_555
covale
1.340
both
B
A
LEU
156
A
C
LEU
157
1_555
A
MSE
157
A
N
MSE
158
1_555
covale
1.333
both
A
A
MSE
157
A
C
MSE
158
1_555
A
SER
158
A
N
SER
159
1_555
covale
1.329
both
B
A
MSE
157
A
C
MSE
158
1_555
A
SER
158
A
N
SER
159
1_555
metalc
2.272
A
HIS
22
A
NE2
HIS
23
1_555
A
FE
191
C
FE
FE
1_555
metalc
2.524
A
HIS
51
A
NE2
HIS
52
1_555
A
FE
191
C
FE
FE
1_555
metalc
2.173
A
ASP
52
A
OD1
ASP
53
1_555
A
FE
190
B
FE
FE
1_555
metalc
2.482
A
ASP
52
A
OD2
ASP
53
1_555
A
FE
191
C
FE
FE
1_555
metalc
2.195
A
HIS
85
A
NE2
HIS
86
1_555
A
FE
190
B
FE
FE
1_555
metalc
2.205
A
HIS
111
A
NE2
HIS
112
1_555
A
FE
190
B
FE
FE
1_555
metalc
2.162
A
ASP
129
A
OD1
ASP
130
1_555
A
FE
191
C
FE
FE
1_555
metalc
2.176
A
FE
190
B
FE
FE
1_555
A
PO4
192
D
O1
PO4
1_555
metalc
2.046
A
FE
190
B
FE
FE
1_555
A
HOH
195
E
O
HOH
1_555
metalc
2.096
A
FE
190
B
FE
FE
1_555
A
HOH
199
E
O
HOH
1_555
metalc
2.358
A
FE
191
C
FE
FE
1_555
A
PO4
192
D
O4
PO4
1_555
metalc
1.711
A
FE
191
C
FE
FE
1_555
A
HOH
195
E
O
HOH
1_555
HYDROLASE
NP_347894.1, predicted HD superfamily hydrolase involved in NAD metabolism, HD domain, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, HYDROLASE
Q97JL1_CLOAB
UNP
1
1
Q97JL1
MWSYDKITDYLMNNLGEKRYKHSLGVMDTAVRLAGIYNEDTEKARIAGLVHDCAKKLPGEKIIEICTNEGYELGDEDIRN
SYLLHGLAGRILAKKVIGIDDEDVLNAIEFHTTGRPNMSLLEKIIYIADYIEPGREFKGVDELRKAADEDLNKALLMSFD
NTIKFVIDKGGFLHHNTIEARNYLISRKG
1
189
3CCG
1
189
Q97JL1
A
1
2
190
1
expression tag
GLY
0
3CCG
A
Q97JL1
UNP
1
BINDING SITE FOR RESIDUE FE A 190
A
FE
190
Software
5
BINDING SITE FOR RESIDUE FE A 191
A
FE
191
Software
5
BINDING SITE FOR RESIDUE PO4 A 192
A
PO4
192
Software
15
A
ASP
52
A
ASP
53
5
1_555
A
HIS
85
A
HIS
86
5
1_555
A
HIS
111
A
HIS
112
5
1_555
A
HOH
195
E
HOH
5
1_555
A
HOH
199
E
HOH
5
1_555
A
HIS
22
A
HIS
23
5
1_555
A
HIS
51
A
HIS
52
5
1_555
A
ASP
52
A
ASP
53
5
1_555
A
ASP
129
A
ASP
130
5
1_555
A
HOH
195
E
HOH
5
1_555
A
ARG
19
A
ARG
20
15
1_555
A
HIS
22
A
HIS
23
15
1_555
A
ASP
52
A
ASP
53
15
1_555
A
LYS
55
A
LYS
56
15
1_555
A
GLU
60
A
GLU
61
15
4_555
A
GLU
64
A
GLU
65
15
4_555
A
HIS
85
A
HIS
86
15
1_555
A
ASP
129
A
ASP
130
15
1_555
A
ARG
135
A
ARG
136
15
1_555
A
HOH
195
E
HOH
15
1_555
A
HOH
199
E
HOH
15
1_555
A
HOH
201
E
HOH
15
4_555
A
HOH
246
E
HOH
15
4_555
A
HOH
250
E
HOH
15
1_555
A
HOH
261
E
HOH
15
4_555
5
C 1 2 1