0.021038
0.000000
0.000000
0.000000
0.021038
0.000000
0.000000
0.000000
0.015936
0.000000
0.000000
0.000000
Caro, J.A.
Flores, E.
Schlessman, J.L.
Heroux, A.
Garcia-Moreno E., B.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
90.000
90.000
47.532
47.532
62.751
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
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
C6 H14 O2
118.174
(4S)-2-METHYL-2,4-PENTANEDIOL
non-polymer
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
C10 H16 N2 O11 P2
402.188
THYMIDINE-3',5'-DIPHOSPHATE
DNA 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
CA
N
75
N
N
N
76
S
C
N
77
N
C
N
78
N
O
N
79
N
C
N
80
N
C
N
81
N
C
N
82
N
O
N
83
N
N
N
84
N
O
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
H
N
95
N
N
N
96
S
C
N
97
N
C
N
98
N
O
N
99
N
C
N
100
N
C
N
101
N
C
N
102
N
O
N
103
N
O
N
104
N
O
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
H
N
114
N
N
N
115
N
C
N
116
N
C
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
N
N
125
S
C
N
126
N
C
N
127
N
O
N
128
N
C
Y
129
N
C
Y
130
N
N
Y
131
N
C
Y
132
N
C
Y
133
N
N
N
134
N
O
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
H
N
145
N
O
N
146
N
H
N
147
N
H
N
148
N
N
N
149
S
C
N
150
N
C
N
151
N
O
N
152
S
C
N
153
N
C
N
154
N
C
N
155
N
C
N
156
N
O
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
H
N
170
N
N
N
171
S
C
N
172
N
C
N
173
N
O
N
174
N
C
N
175
N
C
N
176
N
C
N
177
N
C
N
178
N
O
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
H
N
192
N
N
N
193
S
C
N
194
N
C
N
195
N
O
N
196
N
C
N
197
N
C
N
198
N
C
N
199
N
C
N
200
N
N
N
201
N
O
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
H
N
217
N
N
N
218
S
C
N
219
N
C
N
220
N
O
N
221
N
C
N
222
N
C
N
223
N
S
N
224
N
C
N
225
N
O
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
H
N
237
N
C
N
238
N
C
N
239
N
O
N
240
N
C
N
241
N
C
N
242
S
C
N
243
N
O
N
244
N
C
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
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
N
N
260
S
C
N
261
N
C
N
262
N
O
N
263
N
C
Y
264
N
C
Y
265
N
C
Y
266
N
C
Y
267
N
C
Y
268
N
C
Y
269
N
C
N
270
N
O
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
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
P
N
283
N
O
N
284
N
O
N
285
N
O
N
286
N
O
N
287
N
N
N
288
S
C
N
289
N
C
N
290
N
O
N
291
N
C
N
292
N
C
N
293
N
C
N
294
N
O
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
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
N
C
N
309
N
O
N
310
N
O
N
311
N
H
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
P
N
319
N
O
N
320
N
O
N
321
N
O
N
322
N
P
N
323
N
O
N
324
N
O
N
325
N
O
N
326
N
O
N
327
N
C
N
328
R
C
N
329
N
O
N
330
S
C
N
331
N
O
N
332
N
C
N
333
R
C
N
334
N
N
N
335
N
C
N
336
N
O
N
337
N
N
N
338
N
C
N
339
N
O
N
340
N
C
N
341
N
C
N
342
N
C
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
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
R
C
N
364
N
O
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
N
N
377
S
C
N
378
N
C
N
379
N
O
N
380
N
C
Y
381
N
C
Y
382
N
C
Y
383
N
C
Y
384
N
N
Y
385
N
C
Y
386
N
C
Y
387
N
C
Y
388
N
C
Y
389
N
C
N
390
N
O
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
N
N
404
S
C
N
405
N
C
N
406
N
O
N
407
N
C
Y
408
N
C
Y
409
N
C
Y
410
N
C
Y
411
N
C
Y
412
N
C
Y
413
N
C
N
414
N
O
N
415
N
O
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
N
N
428
S
C
N
429
N
C
N
430
N
O
N
431
N
C
N
432
N
C
N
433
N
C
N
434
N
O
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
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
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
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
doub
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
Y
256
N
doub
Y
257
N
sing
Y
258
N
sing
N
259
N
sing
Y
260
N
doub
N
261
N
sing
Y
262
N
doub
N
263
N
sing
Y
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
doub
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
doub
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
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
doub
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
doub
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
doub
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
sing
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
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
doub
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
doub
N
337
N
sing
N
338
N
sing
N
339
N
doub
N
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
doub
N
351
N
sing
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
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
doub
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
Y
371
N
doub
Y
372
N
sing
Y
373
N
sing
N
374
N
sing
Y
375
N
doub
Y
376
N
sing
Y
377
N
sing
N
378
N
sing
Y
379
N
sing
Y
380
N
doub
N
381
N
sing
Y
382
N
doub
N
383
N
sing
Y
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
doub
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
Y
399
N
doub
Y
400
N
sing
Y
401
N
sing
N
402
N
sing
Y
403
N
doub
N
404
N
sing
Y
405
N
doub
N
406
N
sing
Y
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
doub
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
To be Published
0353
Pressure effects on proteins
10.2210/pdb4k6d/pdb
pdb_00004k6d
100
1
Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification
PIXEL
2013-04-01
DECTRIS PILATUS 6M
Double crystal Si(111) with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification
SINGLE WAVELENGTH
M
x-ray
1
1.1000
1.0
X25
NSLS
1.1000
SYNCHROTRON
NSLS BEAMLINE X25
16921.465
Thermonuclease
3.1.31.1
Nuclease A (UNP residues 83-231)
V23M,T62F
1
man
polymer
402.188
THYMIDINE-3',5'-DIPHOSPHATE
1
syn
non-polymer
40.078
CALCIUM ION
1
syn
non-polymer
118.174
(4S)-2-METHYL-2,4-PENTANEDIOL
2
syn
non-polymer
94.971
PHOSPHATE ION
1
syn
non-polymer
18.015
water
80
nat
water
TNase, Micrococcal nuclease, Staphylococcal nuclease
no
no
ATSTKKLHKEPATLIKAIDGDTMKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFFKKMVENAKKIEVEFDKGQ
RTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQ
ATSTKKLHKEPATLIKAIDGDTMKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFFKKMVENAKKIEVEFDKGQ
RTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQ
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
sample
nuc
1280
Staphylococcus aureus
469008
Escherichia coli
BL21(DE3)
plasmid
pET24a+
1
2.09
41.28
VAPOR DIFFUSION, HANGING DROP
6.0
34% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 6.0, 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
Data collection
Database references
Derived calculations
Refinement description
1
0
2013-04-24
1
1
2023-09-20
_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.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.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.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_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 Angstroms
Crystal structure of staphylococcal nuclease variant V23M/L25F/T62F at cryogenic temperature
Crystal structure of staphylococcal nuclease variant V23M/L36F at cryogenic temperature
RCSB
Y
RCSB
2013-04-15
REL
REL
THP
THYMIDINE-3',5'-DIPHOSPHATE
CA
CALCIUM ION
MPD
(4S)-2-METHYL-2,4-PENTANEDIOL
PO4
PHOSPHATE ION
HOH
water
1SNC
PDB ENTRY 1SNC
PDB
experimental model
THP
1
2
THP
THP
201
A
CA
1
3
CA
CA
202
A
MPD
1
4
MPD
MPD
203
A
PO4
1
5
PO4
PO4
204
A
MPD
1
4
MPD
MPD
205
A
HOH
1
6
HOH
HOH
301
A
HOH
2
6
HOH
HOH
302
A
HOH
3
6
HOH
HOH
303
A
HOH
4
6
HOH
HOH
304
A
HOH
5
6
HOH
HOH
305
A
HOH
6
6
HOH
HOH
306
A
HOH
7
6
HOH
HOH
307
A
HOH
8
6
HOH
HOH
308
A
HOH
9
6
HOH
HOH
309
A
HOH
11
6
HOH
HOH
310
A
HOH
12
6
HOH
HOH
311
A
HOH
13
6
HOH
HOH
312
A
HOH
14
6
HOH
HOH
313
A
HOH
15
6
HOH
HOH
314
A
HOH
16
6
HOH
HOH
315
A
HOH
17
6
HOH
HOH
316
A
HOH
18
6
HOH
HOH
317
A
HOH
19
6
HOH
HOH
318
A
HOH
20
6
HOH
HOH
319
A
HOH
21
6
HOH
HOH
320
A
HOH
22
6
HOH
HOH
321
A
HOH
23
6
HOH
HOH
322
A
HOH
25
6
HOH
HOH
323
A
HOH
26
6
HOH
HOH
324
A
HOH
27
6
HOH
HOH
325
A
HOH
28
6
HOH
HOH
326
A
HOH
29
6
HOH
HOH
327
A
HOH
30
6
HOH
HOH
328
A
HOH
31
6
HOH
HOH
329
A
HOH
32
6
HOH
HOH
330
A
HOH
33
6
HOH
HOH
331
A
HOH
34
6
HOH
HOH
332
A
HOH
35
6
HOH
HOH
333
A
HOH
36
6
HOH
HOH
334
A
HOH
37
6
HOH
HOH
335
A
HOH
38
6
HOH
HOH
336
A
HOH
39
6
HOH
HOH
337
A
HOH
40
6
HOH
HOH
338
A
HOH
41
6
HOH
HOH
339
A
HOH
42
6
HOH
HOH
340
A
HOH
43
6
HOH
HOH
341
A
HOH
45
6
HOH
HOH
342
A
HOH
47
6
HOH
HOH
343
A
HOH
49
6
HOH
HOH
344
A
HOH
50
6
HOH
HOH
345
A
HOH
52
6
HOH
HOH
346
A
HOH
53
6
HOH
HOH
347
A
HOH
54
6
HOH
HOH
348
A
HOH
55
6
HOH
HOH
349
A
HOH
56
6
HOH
HOH
350
A
HOH
57
6
HOH
HOH
351
A
HOH
58
6
HOH
HOH
352
A
HOH
59
6
HOH
HOH
353
A
HOH
60
6
HOH
HOH
354
A
HOH
61
6
HOH
HOH
355
A
HOH
62
6
HOH
HOH
356
A
HOH
63
6
HOH
HOH
357
A
HOH
64
6
HOH
HOH
358
A
HOH
65
6
HOH
HOH
359
A
HOH
66
6
HOH
HOH
360
A
HOH
67
6
HOH
HOH
361
A
HOH
68
6
HOH
HOH
362
A
HOH
69
6
HOH
HOH
363
A
HOH
70
6
HOH
HOH
364
A
HOH
71
6
HOH
HOH
365
A
HOH
72
6
HOH
HOH
366
A
HOH
73
6
HOH
HOH
367
A
HOH
74
6
HOH
HOH
368
A
HOH
75
6
HOH
HOH
369
A
HOH
76
6
HOH
HOH
370
A
HOH
77
6
HOH
HOH
371
A
HOH
78
6
HOH
HOH
372
A
HOH
79
6
HOH
HOH
373
A
HOH
80
6
HOH
HOH
374
A
HOH
81
6
HOH
HOH
375
A
HOH
82
6
HOH
HOH
376
A
HOH
83
6
HOH
HOH
377
A
HOH
84
6
HOH
HOH
378
A
HOH
85
6
HOH
HOH
379
A
HOH
86
6
HOH
HOH
380
A
2.500
37.890
Phaser MODE: MR_AUTO
n
1
1
A
n
2
2
A
n
3
3
A
n
4
4
A
n
5
5
A
LYS
6
n
6
LYS
6
A
LEU
7
n
7
LEU
7
A
HIS
8
n
8
HIS
8
A
LYS
9
n
9
LYS
9
A
GLU
10
n
10
GLU
10
A
PRO
11
n
11
PRO
11
A
ALA
12
n
12
ALA
12
A
THR
13
n
13
THR
13
A
LEU
14
n
14
LEU
14
A
ILE
15
n
15
ILE
15
A
LYS
16
n
16
LYS
16
A
ALA
17
n
17
ALA
17
A
ILE
18
n
18
ILE
18
A
ASP
19
n
19
ASP
19
A
GLY
20
n
20
GLY
20
A
ASP
21
n
21
ASP
21
A
THR
22
n
22
THR
22
A
MET
23
n
23
MET
23
A
LYS
24
n
24
LYS
24
A
LEU
25
n
25
LEU
25
A
MET
26
n
26
MET
26
A
TYR
27
n
27
TYR
27
A
LYS
28
n
28
LYS
28
A
GLY
29
n
29
GLY
29
A
GLN
30
n
30
GLN
30
A
PRO
31
n
31
PRO
31
A
MET
32
n
32
MET
32
A
THR
33
n
33
THR
33
A
PHE
34
n
34
PHE
34
A
ARG
35
n
35
ARG
35
A
LEU
36
n
36
LEU
36
A
LEU
37
n
37
LEU
37
A
LEU
38
n
38
LEU
38
A
VAL
39
n
39
VAL
39
A
ASP
40
n
40
ASP
40
A
THR
41
n
41
THR
41
A
PRO
42
n
42
PRO
42
A
n
43
43
A
n
44
44
A
n
45
45
A
n
46
46
A
n
47
47
A
n
48
48
A
n
49
49
A
n
50
50
A
n
51
51
A
n
52
52
A
n
53
53
A
TYR
54
n
54
TYR
54
A
GLY
55
n
55
GLY
55
A
PRO
56
n
56
PRO
56
A
GLU
57
n
57
GLU
57
A
ALA
58
n
58
ALA
58
A
SER
59
n
59
SER
59
A
ALA
60
n
60
ALA
60
A
PHE
61
n
61
PHE
61
A
PHE
62
n
62
PHE
62
A
LYS
63
n
63
LYS
63
A
LYS
64
n
64
LYS
64
A
MET
65
n
65
MET
65
A
VAL
66
n
66
VAL
66
A
GLU
67
n
67
GLU
67
A
ASN
68
n
68
ASN
68
A
ALA
69
n
69
ALA
69
A
LYS
70
n
70
LYS
70
A
LYS
71
n
71
LYS
71
A
ILE
72
n
72
ILE
72
A
GLU
73
n
73
GLU
73
A
VAL
74
n
74
VAL
74
A
GLU
75
n
75
GLU
75
A
PHE
76
n
76
PHE
76
A
ASP
77
n
77
ASP
77
A
LYS
78
n
78
LYS
78
A
GLY
79
n
79
GLY
79
A
GLN
80
n
80
GLN
80
A
ARG
81
n
81
ARG
81
A
THR
82
n
82
THR
82
A
ASP
83
n
83
ASP
83
A
LYS
84
n
84
LYS
84
A
TYR
85
n
85
TYR
85
A
GLY
86
n
86
GLY
86
A
ARG
87
n
87
ARG
87
A
GLY
88
n
88
GLY
88
A
LEU
89
n
89
LEU
89
A
ALA
90
n
90
ALA
90
A
TYR
91
n
91
TYR
91
A
ILE
92
n
92
ILE
92
A
TYR
93
n
93
TYR
93
A
ALA
94
n
94
ALA
94
A
ASP
95
n
95
ASP
95
A
GLY
96
n
96
GLY
96
A
LYS
97
n
97
LYS
97
A
MET
98
n
98
MET
98
A
VAL
99
n
99
VAL
99
A
ASN
100
n
100
ASN
100
A
GLU
101
n
101
GLU
101
A
ALA
102
n
102
ALA
102
A
LEU
103
n
103
LEU
103
A
VAL
104
n
104
VAL
104
A
ARG
105
n
105
ARG
105
A
GLN
106
n
106
GLN
106
A
GLY
107
n
107
GLY
107
A
LEU
108
n
108
LEU
108
A
ALA
109
n
109
ALA
109
A
LYS
110
n
110
LYS
110
A
VAL
111
n
111
VAL
111
A
ALA
112
n
112
ALA
112
A
TYR
113
n
113
TYR
113
A
VAL
114
n
114
VAL
114
A
TYR
115
n
115
TYR
115
A
LYS
116
n
116
LYS
116
A
PRO
117
n
117
PRO
117
A
ASN
118
n
118
ASN
118
A
ASN
119
n
119
ASN
119
A
THR
120
n
120
THR
120
A
HIS
121
n
121
HIS
121
A
GLU
122
n
122
GLU
122
A
GLN
123
n
123
GLN
123
A
HIS
124
n
124
HIS
124
A
LEU
125
n
125
LEU
125
A
ARG
126
n
126
ARG
126
A
LYS
127
n
127
LYS
127
A
SER
128
n
128
SER
128
A
GLU
129
n
129
GLU
129
A
ALA
130
n
130
ALA
130
A
GLN
131
n
131
GLN
131
A
ALA
132
n
132
ALA
132
A
LYS
133
n
133
LYS
133
A
LYS
134
n
134
LYS
134
A
GLU
135
n
135
GLU
135
A
LYS
136
n
136
LYS
136
A
LEU
137
n
137
LEU
137
A
ASN
138
n
138
ASN
138
A
ILE
139
n
139
ILE
139
A
TRP
140
n
140
TRP
140
A
SER
141
n
141
SER
141
A
n
142
142
A
n
143
143
A
n
144
144
A
n
145
145
A
n
146
146
A
n
147
147
A
n
148
148
A
n
149
149
A
author_and_software_defined_assembly
PISA
1
monomeric
A
ASP
21
A
OD1
ASP
21
1_555
A
CA
202
C
CA
CA
1_555
A
ASP
40
A
OD1
ASP
40
1_555
94.2
A
ASP
21
A
OD1
ASP
21
1_555
A
CA
202
C
CA
CA
1_555
A
THR
41
A
O
THR
41
1_555
91.2
A
ASP
40
A
OD1
ASP
40
1_555
A
CA
202
C
CA
CA
1_555
A
THR
41
A
O
THR
41
1_555
78.4
A
ASP
21
A
OD1
ASP
21
1_555
A
CA
202
C
CA
CA
1_555
A
THP
201
B
O4P
THP
1_555
102.3
A
ASP
40
A
OD1
ASP
40
1_555
A
CA
202
C
CA
CA
1_555
A
THP
201
B
O4P
THP
1_555
80.0
A
THR
41
A
O
THR
41
1_555
A
CA
202
C
CA
CA
1_555
A
THP
201
B
O4P
THP
1_555
155.3
A
ASP
21
A
OD1
ASP
21
1_555
A
CA
202
C
CA
CA
1_555
A
HOH
366
G
O
HOH
1_555
77.9
A
ASP
40
A
OD1
ASP
40
1_555
A
CA
202
C
CA
CA
1_555
A
HOH
366
G
O
HOH
1_555
139.0
A
THR
41
A
O
THR
41
1_555
A
CA
202
C
CA
CA
1_555
A
HOH
366
G
O
HOH
1_555
61.9
A
THP
201
B
O4P
THP
1_555
A
CA
202
C
CA
CA
1_555
A
HOH
366
G
O
HOH
1_555
140.9
A
ASP
21
A
OD1
ASP
21
1_555
A
CA
202
C
CA
CA
1_555
A
HOH
367
G
O
HOH
1_555
82.7
A
ASP
40
A
OD1
ASP
40
1_555
A
CA
202
C
CA
CA
1_555
A
HOH
367
G
O
HOH
1_555
153.6
A
THR
41
A
O
THR
41
1_555
A
CA
202
C
CA
CA
1_555
A
HOH
367
G
O
HOH
1_555
127.8
A
THP
201
B
O4P
THP
1_555
A
CA
202
C
CA
CA
1_555
A
HOH
367
G
O
HOH
1_555
75.1
A
HOH
366
G
O
HOH
1_555
A
CA
202
C
CA
CA
1_555
A
HOH
367
G
O
HOH
1_555
66.1
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
O
LYS
97
A
O
LYS
97
A
N
ALA
94
A
N
ALA
94
A
O
TYR
91
A
O
TYR
91
A
N
GLU
75
A
N
GLU
75
A
O
VAL
74
A
O
VAL
74
A
N
GLU
10
A
N
GLU
10
A
N
LYS
16
A
N
LYS
16
A
O
LYS
24
A
O
LYS
24
A
N
LEU
25
A
N
LEU
25
A
O
MET
32
A
O
MET
32
A
N
ARG
35
A
N
ARG
35
A
O
GLY
88
A
O
GLY
88
A
N
ASP
40
A
N
ASP
40
A
O
LYS
110
A
O
LYS
110
1
A
ALA
1
A
ALA
1
1
Y
1
A
THR
2
A
THR
2
1
Y
1
A
SER
3
A
SER
3
1
Y
1
A
THR
4
A
THR
4
1
Y
1
A
LYS
5
A
LYS
5
1
Y
1
A
GLU
43
A
GLU
43
1
Y
1
A
THR
44
A
THR
44
1
Y
1
A
LYS
45
A
LYS
45
1
Y
1
A
HIS
46
A
HIS
46
1
Y
1
A
PRO
47
A
PRO
47
1
Y
1
A
LYS
48
A
LYS
48
1
Y
1
A
LYS
49
A
LYS
49
1
Y
1
A
GLY
50
A
GLY
50
1
Y
1
A
VAL
51
A
VAL
51
1
Y
1
A
GLU
52
A
GLU
52
1
Y
1
A
LYS
53
A
LYS
53
1
Y
1
A
GLU
142
A
GLU
142
1
Y
1
A
ASP
143
A
ASP
143
1
Y
1
A
ASN
144
A
ASN
144
1
Y
1
A
ALA
145
A
ALA
145
1
Y
1
A
ASP
146
A
ASP
146
1
Y
1
A
SER
147
A
SER
147
1
Y
1
A
GLY
148
A
GLY
148
1
Y
1
A
GLN
149
A
GLN
149
1
Y
1
A
ASP
19
-150.62
-150.89
1
A
ASP
21
-141.64
14.15
1
A
ASN
138
53.31
-105.48
69.400
24.8129
10.920
0.8400
0.0000
0.0000
0.8400
0.0000
-1.6900
0.9630
0.9510
HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
U VALUES : REFINED INDIVIDUALLY
0.2131
0.1902
0.1914
0.1914
1.650
47.53
851
16830
16830
5.1
99.95
0.2331
0.2089
1.000
0.300
0.8356
2.0710
0.0710
0.1033
0.0972
RANDOM
1
THROUGHOUT
0.0
0
MOLECULAR REPLACEMENT
0.1030
0.0970
0.8000
0.8000
1.2000
PDB ENTRY 1SNC
MAXIMUM LIKELIHOOD
MASK
1.650
47.53
80
1134
47
0
1007
0.019
0.020
1123
1.825
2.024
1521
6.368
5.000
137
31.775
24.348
46
14.833
15.000
225
8.666
15.000
5
0.117
0.200
164
0.011
0.021
797
0.2950
0.2510
1.693
73
1125
1198
1198
20
99.83
31.9
1.550
50.0
4K6D
20334
20334
0
0
0.065
2.235
1
14.9
12.5
100.0
0.307
1.550
1.580
8.7
1019
1.057
1
12.8
100.0
0.259
1.580
1.610
1025
1.138
1
12.6
100.0
0.242
1.610
1.640
1006
1.116
1
12.0
100.0
0.204
1.640
1.670
993
1.228
1
12.8
100.0
0.196
1.670
1.710
1015
1.243
1
12.8
100.0
0.167
1.710
1.750
1016
1.331
1
12.2
100.0
0.142
1.750
1.790
1021
1.506
1
12.8
100.0
0.127
1.790
1.840
998
1.584
1
13.1
100.0
0.117
1.840
1.890
1006
1.699
1
12.9
100.0
0.104
1.890
1.950
1009
2.005
1
12.1
100.0
0.092
1.950
2.020
1013
2.207
1
12.9
100.0
0.082
2.020
2.100
1020
2.370
1
12.5
100.0
0.078
2.100
2.200
1022
2.662
1
12.4
100.0
0.077
2.200
2.320
1020
2.863
1
12.9
100.0
0.072
2.320
2.460
1007
2.932
1
12.6
100.0
0.067
2.460
2.650
1021
3.178
1
12.2
100.0
0.064
2.650
2.920
1020
3.300
1
12.3
100.0
0.061
2.920
3.340
1015
3.680
1
12.5
100.0
0.056
3.340
4.210
1029
3.909
1
11.9
100.0
0.055
4.210
50.000
1059
3.869
1
11.7
99.9
data scaling
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
SCALEPACK
program
phasing
Randy J. Read
cimr-phaser@lists.cam.ac.uk
Mon Jun 27 09:33:44 2011 (svn )
http://www-structmed.cimr.cam.ac.uk/phaser/
PHASER
program
2.3.0
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
data extraction
PDB
deposit@deposit.rcsb.org
April 22, 2011
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.11
data collection
CBASS
data reduction
HKL-2000
Crystal structure of Staphylococcal nuclease variant V23M/T62F at cryogenic temperature
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
4
N
N
6
N
N
A
GLY
55
A
GLY
55
HELX_P
A
ALA
69
A
ALA
69
1
1
15
A
VAL
99
A
VAL
99
HELX_P
A
GLN
106
A
GLN
106
1
2
8
A
HIS
121
A
HIS
121
HELX_P
A
GLU
135
A
GLU
135
1
3
15
A
LEU
137
A
LEU
137
HELX_P
A
SER
141
A
SER
141
5
4
5
metalc
2.619
A
ASP
21
A
OD1
ASP
21
1_555
A
CA
202
C
CA
CA
1_555
metalc
2.535
A
ASP
40
A
OD1
ASP
40
1_555
A
CA
202
C
CA
CA
1_555
metalc
2.994
A
THR
41
A
O
THR
41
1_555
A
CA
202
C
CA
CA
1_555
metalc
2.967
A
THP
201
B
O4P
THP
1_555
A
CA
202
C
CA
CA
1_555
metalc
2.937
A
CA
202
C
CA
CA
1_555
A
HOH
366
G
O
HOH
1_555
metalc
2.749
A
CA
202
C
CA
CA
1_555
A
HOH
367
G
O
HOH
1_555
HYDROLASE
Staphylococcal nuclease, hyperstable variant, pdtp, cavity, pressure, HYDROLASE
A
LYS
116
A
LYS
116
1
A
PRO
117
A
PRO
117
4.63
NUC_STAAU
UNP
1
83
P00644
ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQ
RTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQ
83
231
4K6D
1
149
P00644
A
1
1
149
1
VAL
engineered mutation
MET
23
4K6D
A
P00644
UNP
105
23
1
THR
engineered mutation
PHE
62
4K6D
A
P00644
UNP
144
62
7
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
A
LYS
97
A
LYS
97
A
MET
98
A
MET
98
A
GLY
88
A
GLY
88
A
ALA
94
A
ALA
94
A
ILE
72
A
ILE
72
A
GLU
75
A
GLU
75
A
GLU
10
A
GLU
10
A
ALA
17
A
ALA
17
A
THR
22
A
THR
22
A
TYR
27
A
TYR
27
A
GLN
30
A
GLN
30
A
LEU
36
A
LEU
36
A
GLY
88
A
GLY
88
A
ALA
94
A
ALA
94
A
VAL
39
A
VAL
39
A
ASP
40
A
ASP
40
A
LYS
110
A
LYS
110
A
VAL
111
A
VAL
111
BINDING SITE FOR RESIDUE THP A 201
A
THP
201
Software
15
BINDING SITE FOR RESIDUE CA A 202
A
CA
202
Software
6
BINDING SITE FOR RESIDUE MPD A 203
A
MPD
203
Software
5
BINDING SITE FOR RESIDUE MPD A 205
A
MPD
205
Software
3
A
ARG
35
A
ARG
35
15
1_555
A
ASP
40
A
ASP
40
15
1_555
A
LYS
71
A
LYS
71
15
3_555
A
LYS
84
A
LYS
84
15
1_555
A
TYR
85
A
TYR
85
15
1_555
A
ARG
87
A
ARG
87
15
1_555
A
LEU
89
A
LEU
89
15
1_555
A
TYR
113
A
TYR
113
15
1_555
A
TYR
115
A
TYR
115
15
1_555
A
CA
202
C
CA
15
1_555
A
HOH
306
G
HOH
15
1_555
A
HOH
312
G
HOH
15
1_555
A
HOH
330
G
HOH
15
1_555
A
HOH
367
G
HOH
15
1_555
A
HOH
376
G
HOH
15
1_555
A
ASP
21
A
ASP
21
6
1_555
A
ASP
40
A
ASP
40
6
1_555
A
THR
41
A
THR
41
6
1_555
A
THP
201
B
THP
6
1_555
A
HOH
366
G
HOH
6
1_555
A
HOH
367
G
HOH
6
1_555
A
LEU
14
A
LEU
14
5
1_555
A
ILE
15
A
ILE
15
5
1_555
A
LYS
24
A
LYS
24
5
4_554
A
GLU
67
A
GLU
67
5
1_555
A
HOH
305
G
HOH
5
1_555
A
PHE
61
A
PHE
61
3
1_555
A
LYS
116
A
LYS
116
3
2_544
A
HOH
373
G
HOH
3
1_555
76
P 41