0.032157
0.000000
0.002497
0.000000
0.016488
0.000000
0.000000
0.000000
0.027147
0.00000
0.00000
0.00000
Khangulov, V.
Schlessman, J.L.
Garcia-Moreno, B.E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.00
94.44
90.00
31.097
60.651
36.948
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
US
Proteins
PSFGEY
0867
0887-3585
77
570
588
10.1002/prot.22470
19533744
Molecular determinants of the pK(a) values of Asp and Glu residues in staphylococcal nuclease.
2009
10.2210/pdb3bdc/pdb
pdb_00003bdc
110
1
multi-layer optics
CCD
2007-09-05
BRUKER APEX II
GE111
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
SEALED TUBE
OTHER
16143.463
Thermonuclease
3.1.31.1
G50F/V51N/P117G/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
106
nat
water
TNase, Micrococcal nuclease, Staphylococcal nuclease
no
no
ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPEFNEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYG
RGLAYIYADGKMVNEALVRQGLAKVAYVYKGNNTHEQLLRKAEAQAKKEKLNIWSEDNADSGQ
ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPEFNEKYGPEASAFTKKMVENAKKIEVEFDKGQRTDKYG
RGLAYIYADGKMVNEALVRQGLAKVAYVYKGNNTHEQLLRKAEAQAKKEKLNIWSEDNADSGQ
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
Staphylococcus aureus
Escherichia coli
BL21(DE3)
plasmid
pET24a+
1
2.15
42.84
VAPOR DIFFUSION, HANGING DROP
8.0
17% MPD, 25 mM Potassium Phosphate, Calcium Chloride, pdTp, pH 8.0, vapor diffusion, hanging drop, temperature 277K
277
database_2
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Database references
Derived calculations
Data collection
Refinement description
1
0
2008-11-04
1
1
2011-07-13
1
2
2021-10-20
1
3
2023-08-30
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_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
2007-11-14
REL
REL
CA
CALCIUM ION
THP
THYMIDINE-3',5'-DIPHOSPHATE
HOH
water
1TQO
1TQO.PDB where all waters removed, all Bs=20.0 A^2, and E92A
PDB
experimental model
CA
1
2
CA
CA
150
A
THP
142
3
THP
THP
151
A
HOH
1
4
HOH
HOH
152
A
HOH
2
4
HOH
HOH
153
A
HOH
3
4
HOH
HOH
154
A
HOH
4
4
HOH
HOH
155
A
HOH
5
4
HOH
HOH
156
A
HOH
6
4
HOH
HOH
157
A
HOH
7
4
HOH
HOH
158
A
HOH
8
4
HOH
HOH
159
A
HOH
9
4
HOH
HOH
160
A
HOH
10
4
HOH
HOH
161
A
HOH
11
4
HOH
HOH
162
A
HOH
12
4
HOH
HOH
163
A
HOH
13
4
HOH
HOH
164
A
HOH
14
4
HOH
HOH
165
A
HOH
15
4
HOH
HOH
166
A
HOH
16
4
HOH
HOH
167
A
HOH
17
4
HOH
HOH
168
A
HOH
18
4
HOH
HOH
169
A
HOH
19
4
HOH
HOH
170
A
HOH
20
4
HOH
HOH
171
A
HOH
21
4
HOH
HOH
172
A
HOH
22
4
HOH
HOH
173
A
HOH
23
4
HOH
HOH
174
A
HOH
24
4
HOH
HOH
175
A
HOH
25
4
HOH
HOH
176
A
HOH
26
4
HOH
HOH
177
A
HOH
27
4
HOH
HOH
178
A
HOH
28
4
HOH
HOH
179
A
HOH
29
4
HOH
HOH
180
A
HOH
30
4
HOH
HOH
181
A
HOH
31
4
HOH
HOH
182
A
HOH
32
4
HOH
HOH
183
A
HOH
33
4
HOH
HOH
184
A
HOH
34
4
HOH
HOH
185
A
HOH
35
4
HOH
HOH
186
A
HOH
36
4
HOH
HOH
187
A
HOH
37
4
HOH
HOH
188
A
HOH
38
4
HOH
HOH
189
A
HOH
39
4
HOH
HOH
190
A
HOH
40
4
HOH
HOH
191
A
HOH
41
4
HOH
HOH
192
A
HOH
42
4
HOH
HOH
193
A
HOH
43
4
HOH
HOH
194
A
HOH
44
4
HOH
HOH
195
A
HOH
45
4
HOH
HOH
196
A
HOH
46
4
HOH
HOH
197
A
HOH
47
4
HOH
HOH
198
A
HOH
48
4
HOH
HOH
199
A
HOH
49
4
HOH
HOH
200
A
HOH
50
4
HOH
HOH
201
A
HOH
51
4
HOH
HOH
202
A
HOH
52
4
HOH
HOH
203
A
HOH
53
4
HOH
HOH
204
A
HOH
54
4
HOH
HOH
205
A
HOH
55
4
HOH
HOH
206
A
HOH
56
4
HOH
HOH
207
A
HOH
57
4
HOH
HOH
208
A
HOH
58
4
HOH
HOH
209
A
HOH
59
4
HOH
HOH
210
A
HOH
60
4
HOH
HOH
211
A
HOH
61
4
HOH
HOH
212
A
HOH
62
4
HOH
HOH
213
A
HOH
63
4
HOH
HOH
214
A
HOH
64
4
HOH
HOH
215
A
HOH
65
4
HOH
HOH
216
A
HOH
66
4
HOH
HOH
217
A
HOH
67
4
HOH
HOH
218
A
HOH
68
4
HOH
HOH
219
A
HOH
69
4
HOH
HOH
220
A
HOH
70
4
HOH
HOH
221
A
HOH
71
4
HOH
HOH
222
A
HOH
72
4
HOH
HOH
223
A
HOH
73
4
HOH
HOH
224
A
HOH
74
4
HOH
HOH
225
A
HOH
75
4
HOH
HOH
226
A
HOH
76
4
HOH
HOH
227
A
HOH
77
4
HOH
HOH
228
A
HOH
78
4
HOH
HOH
229
A
HOH
79
4
HOH
HOH
230
A
HOH
80
4
HOH
HOH
231
A
HOH
81
4
HOH
HOH
232
A
HOH
82
4
HOH
HOH
233
A
HOH
83
4
HOH
HOH
234
A
HOH
84
4
HOH
HOH
235
A
HOH
85
4
HOH
HOH
236
A
HOH
86
4
HOH
HOH
237
A
HOH
87
4
HOH
HOH
238
A
HOH
88
4
HOH
HOH
239
A
HOH
89
4
HOH
HOH
240
A
HOH
90
4
HOH
HOH
241
A
HOH
91
4
HOH
HOH
242
A
HOH
92
4
HOH
HOH
243
A
HOH
93
4
HOH
HOH
244
A
HOH
94
4
HOH
HOH
245
A
HOH
95
4
HOH
HOH
246
A
HOH
96
4
HOH
HOH
247
A
HOH
97
4
HOH
HOH
248
A
HOH
98
4
HOH
HOH
249
A
HOH
99
4
HOH
HOH
250
A
HOH
100
4
HOH
HOH
251
A
HOH
101
4
HOH
HOH
252
A
HOH
102
4
HOH
HOH
253
A
HOH
103
4
HOH
HOH
254
A
HOH
104
4
HOH
HOH
255
A
HOH
105
4
HOH
HOH
256
A
HOH
106
4
HOH
HOH
257
A
2.500
2.500
36.840
36.840
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
HIS
121
n
115
HIS
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
author_and_software_defined_assembly
PISA
1
monomeric
A
ASP
21
A
OD2
ASP
21
1_555
A
CA
150
B
CA
CA
1_555
A
ASP
40
A
OD1
ASP
40
1_555
83.4
A
ASP
21
A
OD2
ASP
21
1_555
A
CA
150
B
CA
CA
1_555
A
THR
41
A
O
THR
41
1_555
87.8
A
ASP
40
A
OD1
ASP
40
1_555
A
CA
150
B
CA
CA
1_555
A
THR
41
A
O
THR
41
1_555
75.2
A
ASP
21
A
OD2
ASP
21
1_555
A
CA
150
B
CA
CA
1_555
A
GLU
43
A
OE2
GLU
43
1_555
154.9
A
ASP
40
A
OD1
ASP
40
1_555
A
CA
150
B
CA
CA
1_555
A
GLU
43
A
OE2
GLU
43
1_555
120.6
A
THR
41
A
O
THR
41
1_555
A
CA
150
B
CA
CA
1_555
A
GLU
43
A
OE2
GLU
43
1_555
104.5
A
ASP
21
A
OD2
ASP
21
1_555
A
CA
150
B
CA
CA
1_555
A
HOH
157
D
O
HOH
1_555
76.0
A
ASP
40
A
OD1
ASP
40
1_555
A
CA
150
B
CA
CA
1_555
A
HOH
157
D
O
HOH
1_555
136.4
A
THR
41
A
O
THR
41
1_555
A
CA
150
B
CA
CA
1_555
A
HOH
157
D
O
HOH
1_555
140.3
A
GLU
43
A
OE2
GLU
43
1_555
A
CA
150
B
CA
CA
1_555
A
HOH
157
D
O
HOH
1_555
80.8
A
ASP
21
A
OD2
ASP
21
1_555
A
CA
150
B
CA
CA
1_555
A
HOH
162
D
O
HOH
1_555
78.1
A
ASP
40
A
OD1
ASP
40
1_555
A
CA
150
B
CA
CA
1_555
A
HOH
162
D
O
HOH
1_555
137.2
A
THR
41
A
O
THR
41
1_555
A
CA
150
B
CA
CA
1_555
A
HOH
162
D
O
HOH
1_555
65.9
A
GLU
43
A
OE2
GLU
43
1_555
A
CA
150
B
CA
CA
1_555
A
HOH
162
D
O
HOH
1_555
87.0
A
HOH
157
D
O
HOH
1_555
A
CA
150
B
CA
CA
1_555
A
HOH
162
D
O
HOH
1_555
75.3
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
93
A
O
TYR
87
A
N
GLU
73
A
N
GLU
67
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
ILE
18
-116.07
-72.98
1
A
TYR
54
70.33
-5.40
1
A
ASN
138
49.96
-100.68
22.944
0.00
0.00
0.01
0.00
0.00
0.01
0.953
0.920
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.25120
0.18950
0.19556
1.80
31.01
1179
12767
10735
9.9
93.32
3.707
0.113
RANDOM
1
isotropic
THROUGHOUT
MOLECULAR REPLACEMENT
0.160
0.159
0.80
0.80
1.20
1TQO.PDB where all waters removed, all Bs=20.0 A^2, and E92A
MAXIMUM LIKELIHOOD
MASK
1.80
31.01
106
1179
26
0
1047
0.017
0.022
1093
1.772
2.006
1474
5.907
5.000
133
34.112
24.894
47
16.675
15.000
214
9.345
15.000
5
0.121
0.200
160
0.006
0.020
789
0.230
0.200
466
0.310
0.200
737
0.139
0.200
119
0.121
0.200
13
0.135
0.200
12
1.110
1.500
662
1.629
2.000
1038
2.535
3.000
490
3.785
4.500
433
0.362
0.273
1.847
83
737
20
85.15
1.8
31.5
3BDC
14206
0
0
0.152
1
51.898
13.180
99.370
1.8
1.9
6.22
0.415
7.86
100
data scaling
http://www.bruker-axs.de/index.html
SAINT
package
phasing
R. J. Read
cimr-phaser@lists.cam.ac.uk
http://www-structmed.cimr.cam.ac.uk/phaser/
PHASER
other
refinement
Murshudov, G.N.
ccp4@dl.ac.uk
Fortran_77
http://www.ccp4.ac.uk/main.html
REFMAC
program
5.2.0019
data extraction
PDB
sw-help@rcsb.rutgers.edu
July 2, 2007
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
3.000
data collection
APEX
data reduction
SAINT
Crystal structure of Staphylococcal nuclease variant Delta+PHS 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
HIS
121
A
HIS
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
2.901
A
ASP
21
A
OD2
ASP
21
1_555
A
CA
150
B
CA
CA
1_555
metalc
2.716
A
ASP
40
A
OD1
ASP
40
1_555
A
CA
150
B
CA
CA
1_555
metalc
2.836
A
THR
41
A
O
THR
41
1_555
A
CA
150
B
CA
CA
1_555
metalc
2.929
A
GLU
43
A
OE2
GLU
43
1_555
A
CA
150
B
CA
CA
1_555
metalc
2.787
A
CA
150
B
CA
CA
1_555
A
HOH
157
D
O
HOH
1_555
metalc
2.656
A
CA
150
B
CA
CA
1_555
A
HOH
162
D
O
HOH
1_555
HYDROLASE
Staphylococcal nuclease, hyperstable variant, hydrolase, pdtp
NUC_STAAW
UNP
1
83
P00644
ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQ
RTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQ
83
231
3BDC
1
149
P00644
A
1
1
143
1
THR
deletion
3BDC
A
P00644
UNP
126
1
LYS
deletion
3BDC
A
P00644
UNP
127
1
HIS
deletion
3BDC
A
P00644
UNP
128
1
PRO
deletion
3BDC
A
P00644
UNP
129
1
LYS
deletion
3BDC
A
P00644
UNP
130
1
LYS
deletion
3BDC
A
P00644
UNP
131
1
GLY
engineered mutation
PHE
50
3BDC
A
P00644
UNP
132
44
1
VAL
engineered mutation
ASN
51
3BDC
A
P00644
UNP
133
45
1
PRO
engineered mutation
GLY
117
3BDC
A
P00644
UNP
199
111
1
HIS
engineered mutation
LEU
124
3BDC
A
P00644
UNP
206
118
1
SER
engineered mutation
ALA
128
3BDC
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
LYS
9
A
LYS
9
A
ASP
19
A
ASP
19
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 150
A
CA
150
Software
7
BINDING SITE FOR RESIDUE THP A 151
A
THP
151
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
151
C
THP
7
1_555
A
HOH
157
D
HOH
7
1_555
A
HOH
162
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
150
B
CA
18
1_555
A
HOH
157
D
HOH
18
1_555
A
HOH
169
D
HOH
18
1_555
A
HOH
177
D
HOH
18
1_555
A
HOH
178
D
HOH
18
1_555
A
HOH
179
D
HOH
18
1_555
A
HOH
185
D
HOH
18
1_555
A
HOH
199
D
HOH
18
1_555
A
HOH
211
D
HOH
18
1_555
4
P 1 21 1