0.025734
0.000000
0.000000
0.000000
0.025734
0.000000
0.000000
0.000000
0.004688
0.00000
0.00000
0.00000
Ipsaro, J.J.
Haase, A.D.
Hannon, G.J.
Joshua-Tor, L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
38.859
38.859
213.310
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
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
O4 W -2
247.838
TUNGSTATE(VI)ION
non-polymer
Zn 2
65.409
ZINC ION
non-polymer
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
N
N
251
S
C
N
252
N
C
N
253
N
O
N
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
N
261
N
O
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
H
N
271
N
H
N
272
N
H
N
273
N
N
N
274
S
C
N
275
N
C
N
276
N
O
N
277
N
C
N
278
N
C
N
279
N
C
N
280
N
O
N
281
N
H
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
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
N
C
N
295
N
O
N
296
N
O
N
297
N
H
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
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
R
C
N
309
N
O
N
310
N
C
N
311
N
O
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
N
N
322
S
C
N
323
N
C
N
324
N
O
N
325
N
C
Y
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
N
Y
330
N
C
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
C
N
335
N
O
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
N
N
349
S
C
N
350
N
C
N
351
N
O
N
352
N
C
Y
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
N
359
N
O
N
360
N
O
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
N
N
373
S
C
N
374
N
C
N
375
N
O
N
376
N
C
N
377
N
C
N
378
N
C
N
379
N
O
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
W
N
392
N
O
N
393
N
O
N
394
N
O
N
395
N
O
N
396
N
ZN
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
N
376
N
doub
N
377
N
doub
N
378
N
sing
N
379
N
sing
UK
Nature
NATUAS
0006
0028-0836
491
279
283
10.1038/nature11502
23064227
The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis.
2012
10.2210/pdb4ggk/pdb
pdb_00004ggk
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
2012-04-14
ADSC QUANTUM 315
Cryogenically cooled double crystal monochromator with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror
SINGLE WAVELENGTH
M
x-ray
1
1.2716
1.0
1.2983
1.0
X29A
NSLS
1.2716, 1.2983
SYNCHROTRON
NSLS BEAMLINE X29A
22342.830
Mitochondrial cardiolipin hydrolase
3.1.4.-
Cytoplasmic domain, UNP residues 31-221
1
man
polymer
65.409
ZINC ION
1
syn
non-polymer
247.838
TUNGSTATE(VI)ION
1
syn
non-polymer
18.015
water
35
nat
water
Choline phosphatase 6, Mitochondrial phospholipase, MitoPLD, Phosphatidylcholine-hydrolyzing phospholipase D6, Phospholipase D6, PLD 6
no
no
MLAGRRPRREVLFFPSQVTCTEALLQAPGLPPGPSGCPCSLPHSESSLSRLLRALLAARSSLELCLFAFSSPQLGRAVQL
LHQRGVRVRVITDCDYMALNGSQIGLLRKAGIQVRHDQDLGYMHHKFAIVDKKVLITGSLNWTTQAIQNNRENVLIMEDT
EYVRLFLEEFERIWEEFDPTKYSFFPQKHRGHLVPR
MLAGRRPRREVLFFPSQVTCTEALLQAPGLPPGPSGCPCSLPHSESSLSRLLRALLAARSSLELCLFAFSSPQLGRAVQL
LHQRGVRVRVITDCDYMALNGSQIGLLRKAGIQVRHDQDLGYMHHKFAIVDKKVLITGSLNWTTQAIQNNRENVLIMEDT
EYVRLFLEEFERIWEEFDPTKYSFFPQKHRGHLVPR
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
n
n
n
mouse
sample
Pld6
10090
Mus musculus
7108
Spodoptera frugiperda
Sf9
baculovirus
pFL
1
1.80
31.74
VAPOR DIFFUSION, HANGING DROP
6.5
50 mM Bis-Tris, pH 6.5, 18% PEG-3350, 2% tascimate, pH 6.0, 1:100 m/m ratio protein:chymotrypsin, VAPOR DIFFUSION, HANGING DROP, temperature 277K
277
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Database references
Data collection
Database references
Derived calculations
Refinement description
1
0
2012-10-10
1
1
2012-12-12
1
2
2023-09-13
_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_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_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.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Crystal structure of Nuc (dsDNAse)
Crystal structure of Nuc (dsDNAse) in complex with tungstate
RCSB
Y
RCSB
2012-08-06
REL
REL
ZN
ZINC ION
WO4
TUNGSTATE(VI)ION
HOH
water
1BYR
PDB entry 1BYR
PDB
experimental model
ZN
210
2
ZN
ZN
301
A
WO4
211
3
WO4
WO4
302
A
HOH
1
4
HOH
HOH
401
A
HOH
2
4
HOH
HOH
402
A
HOH
3
4
HOH
HOH
403
A
HOH
4
4
HOH
HOH
404
A
HOH
5
4
HOH
HOH
405
A
HOH
6
4
HOH
HOH
406
A
HOH
7
4
HOH
HOH
407
A
HOH
8
4
HOH
HOH
408
A
HOH
9
4
HOH
HOH
409
A
HOH
10
4
HOH
HOH
410
A
HOH
11
4
HOH
HOH
411
A
HOH
12
4
HOH
HOH
412
A
HOH
13
4
HOH
HOH
413
A
HOH
14
4
HOH
HOH
414
A
HOH
15
4
HOH
HOH
415
A
HOH
16
4
HOH
HOH
416
A
HOH
17
4
HOH
HOH
417
A
HOH
18
4
HOH
HOH
418
A
HOH
19
4
HOH
HOH
419
A
HOH
20
4
HOH
HOH
420
A
HOH
21
4
HOH
HOH
421
A
HOH
22
4
HOH
HOH
422
A
HOH
23
4
HOH
HOH
423
A
HOH
24
4
HOH
HOH
424
A
HOH
25
4
HOH
HOH
425
A
HOH
26
4
HOH
HOH
426
A
HOH
27
4
HOH
HOH
427
A
HOH
28
4
HOH
HOH
428
A
HOH
29
4
HOH
HOH
429
A
HOH
30
4
HOH
HOH
430
A
HOH
31
4
HOH
HOH
431
A
HOH
32
4
HOH
HOH
432
A
HOH
33
4
HOH
HOH
433
A
HOH
34
4
HOH
HOH
434
A
HOH
35
4
HOH
HOH
435
A
n
1
30
A
n
2
31
A
n
3
32
A
n
4
33
A
n
5
34
A
n
6
35
A
PRO
36
n
7
PRO
36
A
ARG
37
n
8
ARG
37
A
ARG
38
n
9
ARG
38
A
GLU
39
n
10
GLU
39
A
VAL
40
n
11
VAL
40
A
LEU
41
n
12
LEU
41
A
PHE
42
n
13
PHE
42
A
PHE
43
n
14
PHE
43
A
PRO
44
n
15
PRO
44
A
SER
45
n
16
SER
45
A
GLN
46
n
17
GLN
46
A
VAL
47
n
18
VAL
47
A
THR
48
n
19
THR
48
A
CYS
49
n
20
CYS
49
A
THR
50
n
21
THR
50
A
GLU
51
n
22
GLU
51
A
ALA
52
n
23
ALA
52
A
LEU
53
n
24
LEU
53
A
LEU
54
n
25
LEU
54
A
GLN
55
n
26
GLN
55
A
ALA
56
n
27
ALA
56
A
PRO
57
n
28
PRO
57
A
GLY
58
n
29
GLY
58
A
n
30
59
A
n
31
60
A
n
32
61
A
n
33
62
A
n
34
63
A
n
35
64
A
n
36
65
A
CYS
66
n
37
CYS
66
A
PRO
67
n
38
PRO
67
A
CYS
68
n
39
CYS
68
A
SER
69
n
40
SER
69
A
LEU
70
n
41
LEU
70
A
PRO
71
n
42
PRO
71
A
HIS
72
n
43
HIS
72
A
SER
73
n
44
SER
73
A
GLU
74
n
45
GLU
74
A
SER
75
n
46
SER
75
A
SER
76
n
47
SER
76
A
LEU
77
n
48
LEU
77
A
SER
78
n
49
SER
78
A
ARG
79
n
50
ARG
79
A
LEU
80
n
51
LEU
80
A
LEU
81
n
52
LEU
81
A
ARG
82
n
53
ARG
82
A
ALA
83
n
54
ALA
83
A
LEU
84
n
55
LEU
84
A
LEU
85
n
56
LEU
85
A
ALA
86
n
57
ALA
86
A
ALA
87
n
58
ALA
87
A
ARG
88
n
59
ARG
88
A
SER
89
n
60
SER
89
A
SER
90
n
61
SER
90
A
LEU
91
n
62
LEU
91
A
GLU
92
n
63
GLU
92
A
LEU
93
n
64
LEU
93
A
CYS
94
n
65
CYS
94
A
LEU
95
n
66
LEU
95
A
PHE
96
n
67
PHE
96
A
ALA
97
n
68
ALA
97
A
PHE
98
n
69
PHE
98
A
SER
99
n
70
SER
99
A
SER
100
n
71
SER
100
A
PRO
101
n
72
PRO
101
A
GLN
102
n
73
GLN
102
A
LEU
103
n
74
LEU
103
A
GLY
104
n
75
GLY
104
A
ARG
105
n
76
ARG
105
A
ALA
106
n
77
ALA
106
A
VAL
107
n
78
VAL
107
A
GLN
108
n
79
GLN
108
A
LEU
109
n
80
LEU
109
A
LEU
110
n
81
LEU
110
A
HIS
111
n
82
HIS
111
A
GLN
112
n
83
GLN
112
A
ARG
113
n
84
ARG
113
A
GLY
114
n
85
GLY
114
A
VAL
115
n
86
VAL
115
A
ARG
116
n
87
ARG
116
A
VAL
117
n
88
VAL
117
A
ARG
118
n
89
ARG
118
A
VAL
119
n
90
VAL
119
A
ILE
120
n
91
ILE
120
A
THR
121
n
92
THR
121
A
ASP
122
n
93
ASP
122
A
CYS
123
n
94
CYS
123
A
ASP
124
n
95
ASP
124
A
TYR
125
n
96
TYR
125
A
MET
126
n
97
MET
126
A
n
98
127
A
n
99
128
A
n
100
129
A
GLY
130
n
101
GLY
130
A
SER
131
n
102
SER
131
A
GLN
132
n
103
GLN
132
A
ILE
133
n
104
ILE
133
A
GLY
134
n
105
GLY
134
A
LEU
135
n
106
LEU
135
A
LEU
136
n
107
LEU
136
A
ARG
137
n
108
ARG
137
A
LYS
138
n
109
LYS
138
A
ALA
139
n
110
ALA
139
A
GLY
140
n
111
GLY
140
A
ILE
141
n
112
ILE
141
A
GLN
142
n
113
GLN
142
A
VAL
143
n
114
VAL
143
A
ARG
144
n
115
ARG
144
A
HIS
145
n
116
HIS
145
A
ASP
146
n
117
ASP
146
A
GLN
147
n
118
GLN
147
A
ASP
148
n
119
ASP
148
A
LEU
149
n
120
LEU
149
A
GLY
150
n
121
GLY
150
A
TYR
151
n
122
TYR
151
A
MET
152
n
123
MET
152
A
HIS
153
n
124
HIS
153
A
HIS
154
n
125
HIS
154
A
LYS
155
n
126
LYS
155
A
PHE
156
n
127
PHE
156
A
ALA
157
n
128
ALA
157
A
ILE
158
n
129
ILE
158
A
VAL
159
n
130
VAL
159
A
ASP
160
n
131
ASP
160
A
LYS
161
n
132
LYS
161
A
LYS
162
n
133
LYS
162
A
VAL
163
n
134
VAL
163
A
LEU
164
n
135
LEU
164
A
ILE
165
n
136
ILE
165
A
THR
166
n
137
THR
166
A
GLY
167
n
138
GLY
167
A
SER
168
n
139
SER
168
A
LEU
169
n
140
LEU
169
A
ASN
170
n
141
ASN
170
A
TRP
171
n
142
TRP
171
A
THR
172
n
143
THR
172
A
THR
173
n
144
THR
173
A
GLN
174
n
145
GLN
174
A
ALA
175
n
146
ALA
175
A
ILE
176
n
147
ILE
176
A
GLN
177
n
148
GLN
177
A
ASN
178
n
149
ASN
178
A
ASN
179
n
150
ASN
179
A
ARG
180
n
151
ARG
180
A
GLU
181
n
152
GLU
181
A
ASN
182
n
153
ASN
182
A
VAL
183
n
154
VAL
183
A
LEU
184
n
155
LEU
184
A
ILE
185
n
156
ILE
185
A
MET
186
n
157
MET
186
A
GLU
187
n
158
GLU
187
A
ASP
188
n
159
ASP
188
A
THR
189
n
160
THR
189
A
GLU
190
n
161
GLU
190
A
TYR
191
n
162
TYR
191
A
VAL
192
n
163
VAL
192
A
ARG
193
n
164
ARG
193
A
LEU
194
n
165
LEU
194
A
PHE
195
n
166
PHE
195
A
LEU
196
n
167
LEU
196
A
GLU
197
n
168
GLU
197
A
GLU
198
n
169
GLU
198
A
PHE
199
n
170
PHE
199
A
GLU
200
n
171
GLU
200
A
ARG
201
n
172
ARG
201
A
ILE
202
n
173
ILE
202
A
TRP
203
n
174
TRP
203
A
GLU
204
n
175
GLU
204
A
GLU
205
n
176
GLU
205
A
PHE
206
n
177
PHE
206
A
ASP
207
n
178
ASP
207
A
PRO
208
n
179
PRO
208
A
THR
209
n
180
THR
209
A
n
181
210
A
n
182
211
A
n
183
212
A
n
184
213
A
n
185
214
A
n
186
215
A
n
187
216
A
n
188
217
A
n
189
218
A
n
190
219
A
n
191
220
A
n
192
221
A
n
193
222
A
n
194
223
A
n
195
224
A
n
196
225
A
5.2756
-1.1767
-0.1849
2.6755
-0.4657
3.4310
0.0673
0.4078
-0.2012
-0.2536
-0.0997
-0.0417
-0.1366
0.0669
0.0324
0.0484
-0.0124
-0.0006
0.0696
-0.0277
0.0300
refined
-10.3089
-15.4007
-12.2358
X-RAY DIFFRACTION
A
36
A
302
X-RAY DIFFRACTION
1
author_and_software_defined_assembly
PISA
2
dimeric
3180
-17
14370
A
CYS
49
A
SG
CYS
20
1_555
A
ZN
301
B
ZN
ZN
1_555
A
CYS
66
A
SG
CYS
37
1_555
119.3
A
CYS
49
A
SG
CYS
20
1_555
A
ZN
301
B
ZN
ZN
1_555
A
CYS
68
A
SG
CYS
39
1_555
105.2
A
CYS
66
A
SG
CYS
37
1_555
A
ZN
301
B
ZN
ZN
1_555
A
CYS
68
A
SG
CYS
39
1_555
111.5
A
CYS
49
A
SG
CYS
20
1_555
A
ZN
301
B
ZN
ZN
1_555
A
HIS
72
A
NE2
HIS
43
1_555
106.6
A
CYS
66
A
SG
CYS
37
1_555
A
ZN
301
B
ZN
ZN
1_555
A
HIS
72
A
NE2
HIS
43
1_555
102.3
A
CYS
68
A
SG
CYS
39
1_555
A
ZN
301
B
ZN
ZN
1_555
A
HIS
72
A
NE2
HIS
43
1_555
111.8
A
HIS
153
A
NE2
HIS
124
1_555
A
WO4
302
C
W
WO4
1_555
A
WO4
302
C
O1
WO4
1_555
67.7
A
HIS
153
A
NE2
HIS
124
1_555
A
WO4
302
C
W
WO4
1_555
A
WO4
302
C
O2
WO4
1_555
161.9
A
WO4
302
C
O1
WO4
1_555
A
WO4
302
C
W
WO4
1_555
A
WO4
302
C
O2
WO4
1_555
107.2
A
HIS
153
A
NE2
HIS
124
1_555
A
WO4
302
C
W
WO4
1_555
A
WO4
302
C
O3
WO4
1_555
59.7
A
WO4
302
C
O1
WO4
1_555
A
WO4
302
C
W
WO4
1_555
A
WO4
302
C
O3
WO4
1_555
111.2
A
WO4
302
C
O2
WO4
1_555
A
WO4
302
C
W
WO4
1_555
A
WO4
302
C
O3
WO4
1_555
109.6
A
HIS
153
A
NE2
HIS
124
1_555
A
WO4
302
C
W
WO4
1_555
A
WO4
302
C
O4
WO4
1_555
87.7
A
WO4
302
C
O1
WO4
1_555
A
WO4
302
C
W
WO4
1_555
A
WO4
302
C
O4
WO4
1_555
109.1
A
WO4
302
C
O2
WO4
1_555
A
WO4
302
C
W
WO4
1_555
A
WO4
302
C
O4
WO4
1_555
110.2
A
WO4
302
C
O3
WO4
1_555
A
WO4
302
C
W
WO4
1_555
A
WO4
302
C
O4
WO4
1_555
109.7
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
0.0000000000
1.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
7_555
y,x,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
A
N
LEU
41
A
N
LEU
12
A
O
VAL
183
A
O
VAL
154
A
O
MET
186
A
O
MET
157
A
N
LEU
164
A
N
LEU
135
A
O
ILE
165
A
O
ILE
136
A
N
ALA
157
A
N
ALA
128
A
O
PHE
156
A
O
PHE
127
A
N
CYS
94
A
N
CYS
65
A
N
LEU
93
A
N
LEU
64
A
O
ILE
120
A
O
ILE
91
A
N
VAL
119
A
N
VAL
90
A
O
ARG
144
A
O
ARG
115
1
A
WO4
302
C
WO4
1
A
MET
30
A
MET
1
1
Y
1
A
LEU
31
A
LEU
2
1
Y
1
A
ALA
32
A
ALA
3
1
Y
1
A
GLY
33
A
GLY
4
1
Y
1
A
ARG
34
A
ARG
5
1
Y
1
A
ARG
35
A
ARG
6
1
Y
1
A
LEU
59
A
LEU
30
1
Y
1
A
PRO
60
A
PRO
31
1
Y
1
A
PRO
61
A
PRO
32
1
Y
1
A
GLY
62
A
GLY
33
1
Y
1
A
PRO
63
A
PRO
34
1
Y
1
A
SER
64
A
SER
35
1
Y
1
A
GLY
65
A
GLY
36
1
Y
1
A
ALA
127
A
ALA
98
1
Y
1
A
LEU
128
A
LEU
99
1
Y
1
A
ASN
129
A
ASN
100
1
Y
1
A
LYS
210
A
LYS
181
1
Y
1
A
TYR
211
A
TYR
182
1
Y
1
A
SER
212
A
SER
183
1
Y
1
A
PHE
213
A
PHE
184
1
Y
1
A
PHE
214
A
PHE
185
1
Y
1
A
PRO
215
A
PRO
186
1
Y
1
A
GLN
216
A
GLN
187
1
Y
1
A
LYS
217
A
LYS
188
1
Y
1
A
HIS
218
A
HIS
189
1
Y
1
A
ARG
219
A
ARG
190
1
Y
1
A
GLY
220
A
GLY
191
1
Y
1
A
HIS
221
A
HIS
192
1
Y
1
A
LEU
222
A
LEU
193
1
Y
1
A
VAL
223
A
VAL
194
1
Y
1
A
PRO
224
A
PRO
195
1
Y
1
A
ARG
225
A
ARG
196
1
Y
1
A
HIS
72
-102.09
53.85
1
A
SER
89
-145.62
-41.45
41.182
-0.16
0.00
0.00
-0.16
0.00
0.31
0.939
0.928
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.25123
0.20938
0.21144
0.21144
2.10
38.27
514
9676
9676
5.0
99.43
11.951
0.146
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.254
0.202
0.80
0.80
1.40
PDB entry 1BYR
MAXIMUM LIKELIHOOD
MASK
2.10
38.27
35
1357
6
0
1316
0.013
0.021
1352
0.001
0.020
941
1.382
1.967
1818
0.884
3.003
2268
6.462
5.000
161
42.316
22.923
65
14.372
15.000
238
16.486
15.000
14
0.076
0.200
207
0.005
0.020
1465
0.001
0.020
284
0.551
1.500
535
0.132
1.500
219
0.998
2.000
857
1.695
3.000
317
2.779
4.500
292
0.294
0.226
2.157
35
565
642
20
93.46
2.10
40.0
4GGK
10188
0.0
-3.0
1
18.3
5.8
99.5
2.10
2.23
5.6
2879
1
5.8
98.1
data collection
CBASS
phasing
PHASER
refinement
REFMAC
5.5.0072
data reduction
XDS
data scaling
SCALA
Crystal structure of Zucchini from mouse (mZuc / PLD6 / MitoPLD) bound to tungstate
1
N
N
2
N
N
3
N
N
4
N
N
A
SER
75
A
SER
46
HELX_P
A
ALA
86
A
ALA
57
1
1
12
A
SER
100
A
SER
71
HELX_P
A
ARG
113
A
ARG
84
1
2
14
A
SER
131
A
SER
102
HELX_P
A
ALA
139
A
ALA
110
1
3
9
A
THR
172
A
THR
143
HELX_P
A
ASN
179
A
ASN
150
1
4
8
A
ASP
188
A
ASP
159
HELX_P
A
PHE
206
A
PHE
177
1
5
19
metalc
2.292
A
CYS
49
A
SG
CYS
20
1_555
A
ZN
301
B
ZN
ZN
1_555
metalc
2.329
A
CYS
66
A
SG
CYS
37
1_555
A
ZN
301
B
ZN
ZN
1_555
metalc
2.349
A
CYS
68
A
SG
CYS
39
1_555
A
ZN
301
B
ZN
ZN
1_555
metalc
2.093
A
HIS
72
A
NE2
HIS
43
1_555
A
ZN
301
B
ZN
ZN
1_555
metalc
3.034
A
HIS
153
A
NE2
HIS
124
1_555
A
WO4
302
C
W
WO4
1_555
HYDROLASE
piRNA pathway, protein-RNA interactions, piRNA biogenesis, RNA interference, RNAi, HKD motif CCCH zinc finger, nuclease, nucleic acid binding, outer mitochondrial membrane, HYDROLASE
A
PHE
43
A
PHE
14
1
A
PRO
44
A
PRO
15
11.29
PLD6_MOUSE
UNP
1
31
Q5SWZ9
LAGRRPRREVLFFPSQVTCTEALLQAPGLPPGPSGCPCSLPHSESSLSRLLRALLAARSSLELCLFAFSSPQLGRAVQLL
HQRGVRVRVITDCDYMALNGSQIGLLRKAGIQVRHDQDLGYMHHKFAIVDKKVLITGSLNWTTQAIQNNRENVLIMEDTE
YVRLFLEEFERIWEEFDPTKYSFFPQKHRGH
31
221
4GGK
31
221
Q5SWZ9
A
1
2
192
1
expression tag
MET
30
4GGK
A
Q5SWZ9
UNP
1
1
expression tag
LEU
222
4GGK
A
Q5SWZ9
UNP
193
1
expression tag
VAL
223
4GGK
A
Q5SWZ9
UNP
194
1
expression tag
PRO
224
4GGK
A
Q5SWZ9
UNP
195
1
expression tag
ARG
225
4GGK
A
Q5SWZ9
UNP
196
7
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
parallel
A
ARG
38
A
ARG
9
A
PHE
43
A
PHE
14
A
GLU
181
A
GLU
152
A
MET
186
A
MET
157
A
VAL
163
A
VAL
134
A
GLY
167
A
GLY
138
A
LYS
155
A
LYS
126
A
VAL
159
A
VAL
130
A
SER
90
A
SER
61
A
LEU
95
A
LEU
66
A
ARG
116
A
ARG
87
A
THR
121
A
THR
92
A
GLN
142
A
GLN
113
A
HIS
145
A
HIS
116
BINDING SITE FOR RESIDUE ZN A 301
A
ZN
301
Software
4
BINDING SITE FOR RESIDUE WO4 A 302
A
WO4
302
Software
8
A
CYS
49
A
CYS
20
4
1_555
A
CYS
66
A
CYS
37
4
1_555
A
CYS
68
A
CYS
39
4
1_555
A
HIS
72
A
HIS
43
4
1_555
A
PHE
96
A
PHE
67
8
1_555
A
PHE
96
A
PHE
67
8
7_555
A
HIS
153
A
HIS
124
8
1_555
A
HIS
153
A
HIS
124
8
7_555
A
LYS
155
A
LYS
126
8
7_555
A
LYS
155
A
LYS
126
8
1_555
A
ASN
170
A
ASN
141
8
7_555
A
ASN
170
A
ASN
141
8
1_555
96
P 43 21 2