0.032227
0.000000
0.001307
-0.000000
0.016558
0.000000
0.000000
-0.000000
0.026072
0.000000
0.000000
0.000000
Bell-Upp, P.C.
Schlessman, J.L.
Heroux, A.
Garcia-Moreno E., B.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.000
92.320
90.000
31.030
60.395
38.387
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
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
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
N
N
238
S
C
N
239
N
C
N
240
N
O
N
241
N
C
Y
242
N
C
Y
243
N
C
Y
244
N
C
Y
245
N
C
Y
246
N
C
Y
247
N
C
N
248
N
O
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
N
N
261
S
C
N
262
N
C
N
263
N
O
N
264
N
C
N
265
N
C
N
266
N
C
N
267
N
O
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
N
N
278
S
C
N
279
N
C
N
280
N
O
N
281
N
C
N
282
N
O
N
283
N
O
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
P
N
292
N
O
N
293
N
O
N
294
N
O
N
295
N
P
N
296
N
O
N
297
N
O
N
298
N
O
N
299
N
O
N
300
N
C
N
301
R
C
N
302
N
O
N
303
S
C
N
304
N
O
N
305
N
C
N
306
R
C
N
307
N
N
N
308
N
C
N
309
N
O
N
310
N
N
N
311
N
C
N
312
N
O
N
313
N
C
N
314
N
C
N
315
N
C
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
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
N
N
333
S
C
N
334
N
C
N
335
N
O
N
336
R
C
N
337
N
O
N
338
N
C
N
339
N
O
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
H
N
349
N
N
N
350
S
C
N
351
N
C
N
352
N
O
N
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
N
Y
358
N
C
Y
359
N
C
Y
360
N
C
Y
361
N
C
Y
362
N
C
N
363
N
O
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
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
C
Y
385
N
C
Y
386
N
C
N
387
N
O
N
388
N
O
N
389
N
H
N
390
N
H
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
N
N
401
S
C
N
402
N
C
N
403
N
O
N
404
N
C
N
405
N
C
N
406
N
C
N
407
N
O
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
doub
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
doub
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
doub
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
doub
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
doub
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
Y
127
N
sing
Y
128
N
doub
Y
129
N
doub
N
130
N
sing
Y
131
N
sing
N
132
N
sing
Y
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
doub
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
doub
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
doub
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
doub
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
doub
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
Y
235
N
doub
Y
236
N
sing
Y
237
N
sing
N
238
N
sing
Y
239
N
doub
N
240
N
sing
Y
241
N
doub
N
242
N
sing
Y
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
doub
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
doub
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
doub
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
doub
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
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
doub
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
doub
N
312
N
sing
N
313
N
sing
N
314
N
doub
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
doub
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
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
sing
N
341
N
doub
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
Y
346
N
doub
Y
347
N
sing
Y
348
N
sing
N
349
N
sing
Y
350
N
doub
Y
351
N
sing
Y
352
N
sing
N
353
N
sing
Y
354
N
sing
Y
355
N
doub
N
356
N
sing
Y
357
N
doub
N
358
N
sing
Y
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
sing
N
367
N
sing
N
368
N
sing
N
369
N
doub
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
Y
374
N
doub
Y
375
N
sing
Y
376
N
sing
N
377
N
sing
Y
378
N
doub
N
379
N
sing
Y
380
N
doub
N
381
N
sing
Y
382
N
sing
N
383
N
sing
N
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
doub
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
404
N
sing
To be Published
0353
Crystal structure of Staphylococcal nuclease variant Delta+PHS H121E at cryogenic temperature
10.2210/pdb4ial/pdb
pdb_00004ial
100
1
Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification
PIXEL
2012-09-26
DECTRIS PILATUS 6M
double crystal Si(111)
SINGLE WAVELENGTH
M
x-ray
1
1.10
1.0
X25
NSLS
1.10
SYNCHROTRON
NSLS BEAMLINE X25
16134.430
Thermonuclease
3.1.31.1
Nuclease A (UNP residues 83-231)
G50F/V51N/P117G/H121E/H124L/S128A/Del44-49
1
man
polymer
40.078
CALCIUM ION
1
syn
non-polymer
402.188
THYMIDINE-3',5'-DIPHOSPHATE
1
syn
non-polymer
18.015
water
81
nat
water
TNase, Micrococcal nuclease, Staphylococcal nuclease
no
no
ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPEFNEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYG
RGLAYIYADGKMVNEALVRQGLAKVAYVYKGNNTEEQLLRKAEAQAKKEKLNIWSEDNADSGQ
ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPEFNEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYG
RGLAYIYADGKMVNEALVRQGLAKVAYVYKGNNTEEQLLRKAEAQAKKEKLNIWSEDNADSGQ
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
sample
1280
Staphylococcus aureus
469008
Escherichia coli
BL21(DE3)
plasmid
pET24a+
1
2.23
44.78
VAPOR DIFFUSION, HANGING DROP
8
24% MPD, 25 mM potassium phosphate, calcium chloride, pdTp, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
277
software
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
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
2013-01-09
1
1
2017-11-15
1
2
2023-09-20
_software.name
_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
RCSB
Y
RCSB
2012-12-06
REL
REL
CA
CALCIUM ION
THP
THYMIDINE-3',5'-DIPHOSPHATE
HOH
water
3BDC
PDB ENTRY 3BDC
PDB
experimental model
CA
1
2
CA
CA
201
A
THP
1
3
THP
THP
202
A
HOH
1
4
HOH
HOH
301
A
HOH
1
4
HOH
HOH
302
A
HOH
2
4
HOH
HOH
303
A
HOH
3
4
HOH
HOH
304
A
HOH
5
4
HOH
HOH
305
A
HOH
6
4
HOH
HOH
306
A
HOH
7
4
HOH
HOH
307
A
HOH
8
4
HOH
HOH
308
A
HOH
9
4
HOH
HOH
309
A
HOH
10
4
HOH
HOH
310
A
HOH
11
4
HOH
HOH
311
A
HOH
12
4
HOH
HOH
312
A
HOH
13
4
HOH
HOH
313
A
HOH
14
4
HOH
HOH
314
A
HOH
15
4
HOH
HOH
315
A
HOH
16
4
HOH
HOH
316
A
HOH
17
4
HOH
HOH
317
A
HOH
18
4
HOH
HOH
318
A
HOH
19
4
HOH
HOH
319
A
HOH
20
4
HOH
HOH
320
A
HOH
21
4
HOH
HOH
321
A
HOH
22
4
HOH
HOH
322
A
HOH
23
4
HOH
HOH
323
A
HOH
25
4
HOH
HOH
324
A
HOH
26
4
HOH
HOH
325
A
HOH
27
4
HOH
HOH
326
A
HOH
28
4
HOH
HOH
327
A
HOH
30
4
HOH
HOH
328
A
HOH
31
4
HOH
HOH
329
A
HOH
32
4
HOH
HOH
330
A
HOH
33
4
HOH
HOH
331
A
HOH
34
4
HOH
HOH
332
A
HOH
35
4
HOH
HOH
333
A
HOH
38
4
HOH
HOH
334
A
HOH
39
4
HOH
HOH
335
A
HOH
40
4
HOH
HOH
336
A
HOH
41
4
HOH
HOH
337
A
HOH
42
4
HOH
HOH
338
A
HOH
44
4
HOH
HOH
339
A
HOH
45
4
HOH
HOH
340
A
HOH
48
4
HOH
HOH
341
A
HOH
50
4
HOH
HOH
342
A
HOH
51
4
HOH
HOH
343
A
HOH
53
4
HOH
HOH
344
A
HOH
54
4
HOH
HOH
345
A
HOH
55
4
HOH
HOH
346
A
HOH
56
4
HOH
HOH
347
A
HOH
57
4
HOH
HOH
348
A
HOH
59
4
HOH
HOH
349
A
HOH
61
4
HOH
HOH
350
A
HOH
62
4
HOH
HOH
351
A
HOH
63
4
HOH
HOH
352
A
HOH
67
4
HOH
HOH
353
A
HOH
69
4
HOH
HOH
354
A
HOH
70
4
HOH
HOH
355
A
HOH
74
4
HOH
HOH
356
A
HOH
75
4
HOH
HOH
357
A
HOH
77
4
HOH
HOH
358
A
HOH
78
4
HOH
HOH
359
A
HOH
79
4
HOH
HOH
360
A
HOH
81
4
HOH
HOH
361
A
HOH
82
4
HOH
HOH
362
A
HOH
84
4
HOH
HOH
363
A
HOH
85
4
HOH
HOH
364
A
HOH
88
4
HOH
HOH
365
A
HOH
89
4
HOH
HOH
366
A
HOH
90
4
HOH
HOH
367
A
HOH
93
4
HOH
HOH
368
A
HOH
95
4
HOH
HOH
369
A
HOH
96
4
HOH
HOH
370
A
HOH
97
4
HOH
HOH
371
A
HOH
98
4
HOH
HOH
372
A
HOH
100
4
HOH
HOH
373
A
HOH
102
4
HOH
HOH
374
A
HOH
106
4
HOH
HOH
375
A
HOH
114
4
HOH
HOH
376
A
HOH
115
4
HOH
HOH
377
A
HOH
116
4
HOH
HOH
378
A
HOH
120
4
HOH
HOH
379
A
HOH
127
4
HOH
HOH
380
A
HOH
129
4
HOH
HOH
381
A
2.500
2.500
38.360
38.360
Phaser MODE: MR_AUTO
n
1
1
A
n
2
2
A
n
3
3
A
n
4
4
A
n
5
5
A
n
6
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
VAL
23
n
23
VAL
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
GLU
43
n
43
GLU
43
A
PHE
50
n
44
PHE
50
A
ASN
51
n
45
ASN
51
A
GLU
52
n
46
GLU
52
A
LYS
53
n
47
LYS
53
A
TYR
54
n
48
TYR
54
A
GLY
55
n
49
GLY
55
A
PRO
56
n
50
PRO
56
A
GLU
57
n
51
GLU
57
A
ALA
58
n
52
ALA
58
A
SER
59
n
53
SER
59
A
ALA
60
n
54
ALA
60
A
PHE
61
n
55
PHE
61
A
THR
62
n
56
THR
62
A
LYS
63
n
57
LYS
63
A
LYS
64
n
58
LYS
64
A
MET
65
n
59
MET
65
A
VAL
66
n
60
VAL
66
A
GLU
67
n
61
GLU
67
A
ASN
68
n
62
ASN
68
A
ALA
69
n
63
ALA
69
A
LYS
70
n
64
LYS
70
A
LYS
71
n
65
LYS
71
A
ILE
72
n
66
ILE
72
A
GLU
73
n
67
GLU
73
A
VAL
74
n
68
VAL
74
A
GLU
75
n
69
GLU
75
A
PHE
76
n
70
PHE
76
A
ASP
77
n
71
ASP
77
A
LYS
78
n
72
LYS
78
A
GLY
79
n
73
GLY
79
A
GLN
80
n
74
GLN
80
A
ARG
81
n
75
ARG
81
A
THR
82
n
76
THR
82
A
ASP
83
n
77
ASP
83
A
LYS
84
n
78
LYS
84
A
TYR
85
n
79
TYR
85
A
GLY
86
n
80
GLY
86
A
ARG
87
n
81
ARG
87
A
GLY
88
n
82
GLY
88
A
LEU
89
n
83
LEU
89
A
ALA
90
n
84
ALA
90
A
TYR
91
n
85
TYR
91
A
ILE
92
n
86
ILE
92
A
TYR
93
n
87
TYR
93
A
ALA
94
n
88
ALA
94
A
ASP
95
n
89
ASP
95
A
GLY
96
n
90
GLY
96
A
LYS
97
n
91
LYS
97
A
MET
98
n
92
MET
98
A
VAL
99
n
93
VAL
99
A
ASN
100
n
94
ASN
100
A
GLU
101
n
95
GLU
101
A
ALA
102
n
96
ALA
102
A
LEU
103
n
97
LEU
103
A
VAL
104
n
98
VAL
104
A
ARG
105
n
99
ARG
105
A
GLN
106
n
100
GLN
106
A
GLY
107
n
101
GLY
107
A
LEU
108
n
102
LEU
108
A
ALA
109
n
103
ALA
109
A
LYS
110
n
104
LYS
110
A
VAL
111
n
105
VAL
111
A
ALA
112
n
106
ALA
112
A
TYR
113
n
107
TYR
113
A
VAL
114
n
108
VAL
114
A
TYR
115
n
109
TYR
115
A
LYS
116
n
110
LYS
116
A
GLY
117
n
111
GLY
117
A
ASN
118
n
112
ASN
118
A
ASN
119
n
113
ASN
119
A
THR
120
n
114
THR
120
A
GLU
121
n
115
GLU
121
A
GLU
122
n
116
GLU
122
A
GLN
123
n
117
GLN
123
A
LEU
124
n
118
LEU
124
A
LEU
125
n
119
LEU
125
A
ARG
126
n
120
ARG
126
A
LYS
127
n
121
LYS
127
A
ALA
128
n
122
ALA
128
A
GLU
129
n
123
GLU
129
A
ALA
130
n
124
ALA
130
A
GLN
131
n
125
GLN
131
A
ALA
132
n
126
ALA
132
A
LYS
133
n
127
LYS
133
A
LYS
134
n
128
LYS
134
A
GLU
135
n
129
GLU
135
A
LYS
136
n
130
LYS
136
A
LEU
137
n
131
LEU
137
A
ASN
138
n
132
ASN
138
A
ILE
139
n
133
ILE
139
A
TRP
140
n
134
TRP
140
A
SER
141
n
135
SER
141
A
n
136
142
A
n
137
143
A
n
138
144
A
n
139
145
A
n
140
146
A
n
141
147
A
n
142
148
A
n
143
149
A
3.0602
-0.2932
-0.2350
3.1342
0.4745
0.7190
0.0139
0.1195
-0.1262
0.0755
0.0697
-0.1094
0.0839
0.1487
-0.0836
0.1522
0.0283
-0.0043
0.1696
0.0078
0.0273
refined
14.1804
0.1839
4.5964
X-RAY DIFFRACTION
3.2725
-0.0130
0.2185
1.9855
0.4182
1.0089
-0.0096
0.1382
0.1060
0.0043
0.0296
0.1071
0.0629
0.0249
-0.0200
0.1519
0.0062
0.0042
0.1363
0.0207
0.0140
refined
7.1896
5.0497
4.4502
X-RAY DIFFRACTION
12.1285
1.5380
2.6277
7.3776
0.1051
8.0636
-0.2042
-0.2187
0.6924
0.1451
0.0932
0.3877
-0.3545
-0.2443
0.1110
0.1487
0.0431
0.0430
0.1148
-0.0552
0.1686
refined
-0.3160
16.5545
14.7405
X-RAY DIFFRACTION
A
7
A
52
X-RAY DIFFRACTION
1
A
53
A
130
X-RAY DIFFRACTION
2
A
131
A
141
X-RAY DIFFRACTION
3
author_and_software_defined_assembly
PISA
1
monomeric
A
ASP
21
A
OD2
ASP
21
1_555
A
CA
201
B
CA
CA
1_555
A
ASP
40
A
OD1
ASP
40
1_555
82.5
A
ASP
21
A
OD2
ASP
21
1_555
A
CA
201
B
CA
CA
1_555
A
THR
41
A
O
THR
41
1_555
87.5
A
ASP
40
A
OD1
ASP
40
1_555
A
CA
201
B
CA
CA
1_555
A
THR
41
A
O
THR
41
1_555
77.1
A
ASP
21
A
OD2
ASP
21
1_555
A
CA
201
B
CA
CA
1_555
A
GLU
43
A
OE2
GLU
43
1_555
152.7
A
ASP
40
A
OD1
ASP
40
1_555
A
CA
201
B
CA
CA
1_555
A
GLU
43
A
OE2
GLU
43
1_555
124.7
A
THR
41
A
O
THR
41
1_555
A
CA
201
B
CA
CA
1_555
A
GLU
43
A
OE2
GLU
43
1_555
99.6
A
ASP
21
A
OD2
ASP
21
1_555
A
CA
201
B
CA
CA
1_555
A
THP
202
C
O5P
THP
1_555
96.2
A
ASP
40
A
OD1
ASP
40
1_555
A
CA
201
B
CA
CA
1_555
A
THP
202
C
O5P
THP
1_555
69.1
A
THR
41
A
O
THR
41
1_555
A
CA
201
B
CA
CA
1_555
A
THP
202
C
O5P
THP
1_555
145.1
A
GLU
43
A
OE2
GLU
43
1_555
A
CA
201
B
CA
CA
1_555
A
THP
202
C
O5P
THP
1_555
92.8
A
ASP
21
A
OD2
ASP
21
1_555
A
CA
201
B
CA
CA
1_555
A
HOH
304
D
O
HOH
1_555
78.0
A
ASP
40
A
OD1
ASP
40
1_555
A
CA
201
B
CA
CA
1_555
A
HOH
304
D
O
HOH
1_555
138.5
A
THR
41
A
O
THR
41
1_555
A
CA
201
B
CA
CA
1_555
A
HOH
304
D
O
HOH
1_555
65.9
A
GLU
43
A
OE2
GLU
43
1_555
A
CA
201
B
CA
CA
1_555
A
HOH
304
D
O
HOH
1_555
80.9
A
THP
202
C
O5P
THP
1_555
A
CA
201
B
CA
CA
1_555
A
HOH
304
D
O
HOH
1_555
148.8
A
ASP
21
A
OD2
ASP
21
1_555
A
CA
201
B
CA
CA
1_555
A
HOH
305
D
O
HOH
1_555
76.5
A
ASP
40
A
OD1
ASP
40
1_555
A
CA
201
B
CA
CA
1_555
A
HOH
305
D
O
HOH
1_555
135.0
A
THR
41
A
O
THR
41
1_555
A
CA
201
B
CA
CA
1_555
A
HOH
305
D
O
HOH
1_555
139.8
A
GLU
43
A
OE2
GLU
43
1_555
A
CA
201
B
CA
CA
1_555
A
HOH
305
D
O
HOH
1_555
81.3
A
THP
202
C
O5P
THP
1_555
A
CA
201
B
CA
CA
1_555
A
HOH
305
D
O
HOH
1_555
74.1
A
HOH
304
D
O
HOH
1_555
A
CA
201
B
CA
CA
1_555
A
HOH
305
D
O
HOH
1_555
74.7
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
O
LYS
97
A
O
LYS
91
A
N
ALA
94
A
N
ALA
88
A
O
TYR
91
A
O
TYR
85
A
N
GLU
75
A
N
GLU
69
A
O
VAL
74
A
O
VAL
68
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
VAL
23
A
N
VAL
23
A
O
PHE
34
A
O
PHE
34
A
N
ARG
35
A
N
ARG
35
A
O
GLY
88
A
O
GLY
82
A
N
ASP
40
A
N
ASP
40
A
O
LYS
110
A
O
LYS
104
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
LYS
6
A
LYS
6
1
Y
1
A
GLU
142
A
GLU
136
1
Y
1
A
ASP
143
A
ASP
137
1
Y
1
A
ASN
144
A
ASN
138
1
Y
1
A
ALA
145
A
ALA
139
1
Y
1
A
ASP
146
A
ASP
140
1
Y
1
A
SER
147
A
SER
141
1
Y
1
A
GLY
148
A
GLY
142
1
Y
1
A
GLN
149
A
GLN
143
1
Y
1
A
TYR
54
72.64
-2.37
1
A
ASP
95
39.05
49.36
1
A
ASN
118
-115.43
53.55
1
A
ASN
138
47.70
-100.98
84.510
35.6892
20.160
-3.7400
-0.0000
0.4500
-0.9800
-0.0000
4.6900
0.9680
0.9550
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
U VALUES : WITH TLS ADDED
0.2389
0.1968
0.1989
0.1989
1.595
38.355
944
18430
18430
5.1
97.37
0.2681
0.2184
1.000
1.000
0.7803
4.4290
0.0870
0.0957
0.0999
RANDOM
1
THROUGHOUT
0.0
0
MOLECULAR REPLACEMENT
0.0960
0.1000
0.8000
0.8000
1.2000
PDB ENTRY 3BDC
MAXIMUM LIKELIHOOD
MASK
1.595
38.355
81
1139
26
0
1032
0.018
0.020
1075
0.001
0.020
1060
1.908
2.010
1446
0.840
3.000
2450
6.780
5.000
128
34.275
25.106
47
14.853
15.000
209
18.783
15.000
5
0.124
0.200
155
0.012
0.020
1173
0.001
0.020
226
0.3330
0.2880
1.636
64
1094
1158
20
82.36
34.5
1.595
38.355
4IAL
18439
18439
0
0
0.051
1.763
1
38.332
3.7
97.7
0.261
1.595
1.630
4.010
825
0.973
1
2.8
85.9
0.235
1.630
1.660
847
1.045
1
3.1
93.0
0.231
1.660
1.690
891
0.976
1
3.3
95.5
0.212
1.690
1.720
936
1.018
1
3.8
98.1
0.191
1.720
1.760
910
0.998
1
3.9
98.6
0.167
1.760
1.800
934
1.237
1
3.7
98.4
0.145
1.800
1.850
933
1.302
1
3.9
98.5
0.133
1.850
1.900
910
1.335
1
3.9
98.4
0.110
1.900
1.950
942
1.555
1
3.7
99.1
0.101
1.950
2.020
932
1.505
1
3.8
99.1
0.090
2.020
2.090
927
1.862
1
3.9
98.9
0.084
2.090
2.170
922
2.012
1
3.7
99.1
0.076
2.170
2.270
939
2.011
1
3.9
99.4
0.083
2.270
2.390
947
2.479
1
3.7
99.5
0.072
2.390
2.540
935
2.484
1
4.0
99.2
0.062
2.540
2.740
938
2.308
1
3.8
99.9
0.054
2.740
3.010
944
2.238
1
4.0
99.6
0.048
3.010
3.450
940
2.454
1
3.8
99.1
0.042
3.450
4.340
929
2.234
1
3.8
97.4
0.043
4.340
38.355
958
2.421
1
3.7
98.0
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
DENZO
Crystal structure of Staphylococcal nuclease variant Delta+PHS H121E at cryogenic temperature
1
N
N
2
N
N
3
N
N
4
N
N
A
TYR
54
A
TYR
48
HELX_P
A
ALA
69
A
ALA
63
1
1
16
A
VAL
99
A
VAL
93
HELX_P
A
GLN
106
A
GLN
100
1
2
8
A
GLU
121
A
GLU
115
HELX_P
A
GLU
135
A
GLU
129
1
3
15
A
LEU
137
A
LEU
131
HELX_P
A
SER
141
A
SER
135
5
4
5
metalc
2.839
A
ASP
21
A
OD2
ASP
21
1_555
A
CA
201
B
CA
CA
1_555
metalc
2.617
A
ASP
40
A
OD1
ASP
40
1_555
A
CA
201
B
CA
CA
1_555
metalc
2.842
A
THR
41
A
O
THR
41
1_555
A
CA
201
B
CA
CA
1_555
metalc
2.914
A
GLU
43
A
OE2
GLU
43
1_555
A
CA
201
B
CA
CA
1_555
metalc
3.166
A
CA
201
B
CA
CA
1_555
A
THP
202
C
O5P
THP
1_555
metalc
3.005
A
CA
201
B
CA
CA
1_555
A
HOH
304
D
O
HOH
1_555
metalc
2.838
A
CA
201
B
CA
CA
1_555
A
HOH
305
D
O
HOH
1_555
HYDROLASE
nuclease, hyperstable, pdTp, ion pair, HYDROLASE
NUC_STAAU
UNP
1
83
P00644
ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQ
RTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQ
83
231
4IAL
1
149
P00644
A
1
1
143
1
THR
deletion
4IAL
A
P00644
UNP
126
1
LYS
deletion
4IAL
A
P00644
UNP
127
1
HIS
deletion
4IAL
A
P00644
UNP
128
1
PRO
deletion
4IAL
A
P00644
UNP
129
1
LYS
deletion
4IAL
A
P00644
UNP
130
1
LYS
deletion
4IAL
A
P00644
UNP
131
1
GLY
engineered mutation
PHE
50
4IAL
A
P00644
UNP
132
44
1
VAL
engineered mutation
ASN
51
4IAL
A
P00644
UNP
133
45
1
PRO
engineered mutation
GLY
117
4IAL
A
P00644
UNP
199
111
1
HIS
engineered mutation
GLU
121
4IAL
A
P00644
UNP
203
115
1
HIS
engineered mutation
LEU
124
4IAL
A
P00644
UNP
206
118
1
SER
engineered mutation
ALA
128
4IAL
A
P00644
UNP
210
122
7
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
A
LYS
97
A
LYS
91
A
MET
98
A
MET
92
A
GLY
88
A
GLY
82
A
ALA
94
A
ALA
88
A
ILE
72
A
ILE
66
A
GLU
75
A
GLU
69
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
82
A
ALA
94
A
ALA
88
A
VAL
39
A
VAL
39
A
ASP
40
A
ASP
40
A
LYS
110
A
LYS
104
A
VAL
111
A
VAL
105
BINDING SITE FOR RESIDUE CA A 201
A
CA
201
Software
7
BINDING SITE FOR RESIDUE THP A 202
A
THP
202
Software
18
A
ASP
21
A
ASP
21
7
1_555
A
ASP
40
A
ASP
40
7
1_555
A
THR
41
A
THR
41
7
1_555
A
GLU
43
A
GLU
43
7
1_555
A
THP
202
C
THP
7
1_555
A
HOH
304
D
HOH
7
1_555
A
HOH
305
D
HOH
7
1_555
A
ARG
35
A
ARG
35
18
1_555
A
ASP
40
A
ASP
40
18
1_555
A
LYS
84
A
LYS
78
18
1_555
A
TYR
85
A
TYR
79
18
1_555
A
ARG
87
A
ARG
81
18
1_555
A
LEU
89
A
LEU
83
18
1_555
A
TYR
113
A
TYR
107
18
1_555
A
TYR
115
A
TYR
109
18
1_555
A
LYS
127
A
LYS
121
18
1_655
A
CA
201
B
CA
18
1_555
A
HOH
301
D
HOH
18
1_555
A
HOH
305
D
HOH
18
1_555
A
HOH
313
D
HOH
18
1_555
A
HOH
318
D
HOH
18
1_555
A
HOH
321
D
HOH
18
1_555
A
HOH
335
D
HOH
18
1_555
A
HOH
351
D
HOH
18
1_555
A
HOH
356
D
HOH
18
1_555
4
P 1 21 1