0.020738
0.000000
0.000000
0.000000
0.020738
0.000000
0.000000
0.000000
0.015803
0.000000
0.000000
0.000000
Khangulov, V.S.
Schlessman, J.L.
Garcia-Moreno, E.B.
Benning, M.
Isom, D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
90.000
90.000
48.220
48.220
63.280
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
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
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
N
N
75
S
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
C
N
80
N
C
N
81
N
O
N
82
N
N
N
83
N
O
N
84
N
H
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
N
N
95
S
C
N
96
N
C
N
97
N
O
N
98
N
C
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
O
N
104
N
H
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
N
N
114
N
C
N
115
N
C
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
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
Y
128
N
C
Y
129
N
N
Y
130
N
C
Y
131
N
C
Y
132
N
N
N
133
N
O
N
134
N
H
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
O
N
145
N
H
N
146
N
H
N
147
N
N
N
148
S
C
N
149
N
C
N
150
N
O
N
151
S
C
N
152
N
C
N
153
N
C
N
154
N
C
N
155
N
O
N
156
N
H
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
N
N
170
S
C
N
171
N
C
N
172
N
O
N
173
N
C
N
174
N
C
N
175
N
C
N
176
N
C
N
177
N
O
N
178
N
H
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
N
N
192
S
C
N
193
N
C
N
194
N
O
N
195
N
C
N
196
N
C
N
197
N
C
N
198
N
C
N
199
N
N
N
200
N
O
N
201
N
H
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
N
N
217
S
C
N
218
N
C
N
219
N
O
N
220
N
C
N
221
N
C
N
222
N
S
N
223
N
C
N
224
N
O
N
225
N
H
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
C
N
237
N
C
N
238
N
O
N
239
N
C
N
240
N
C
N
241
S
C
N
242
N
O
N
243
N
C
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
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
N
N
259
S
C
N
260
N
C
N
261
N
O
N
262
N
C
Y
263
N
C
Y
264
N
C
Y
265
N
C
Y
266
N
C
Y
267
N
C
Y
268
N
C
N
269
N
O
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
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
P
N
282
N
O
N
283
N
O
N
284
N
O
N
285
N
O
N
286
N
N
N
287
S
C
N
288
N
C
N
289
N
O
N
290
N
C
N
291
N
C
N
292
N
C
N
293
N
O
N
294
N
H
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
N
N
304
S
C
N
305
N
C
N
306
N
O
N
307
N
C
N
308
N
O
N
309
N
O
N
310
N
H
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
N
N
318
S
C
N
319
N
C
N
320
N
O
N
321
R
C
N
322
N
O
N
323
N
C
N
324
N
O
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
H
N
333
N
H
N
334
N
N
N
335
S
C
N
336
N
C
N
337
N
O
N
338
N
C
Y
339
N
C
Y
340
N
C
Y
341
N
C
Y
342
N
N
Y
343
N
C
Y
344
N
C
Y
345
N
C
Y
346
N
C
Y
347
N
C
N
348
N
O
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
H
N
360
N
H
N
361
N
N
N
362
S
C
N
363
N
C
N
364
N
O
N
365
N
C
Y
366
N
C
Y
367
N
C
Y
368
N
C
Y
369
N
C
Y
370
N
C
Y
371
N
C
N
372
N
O
N
373
N
O
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
N
N
386
S
C
N
387
N
C
N
388
N
O
N
389
N
C
N
390
N
C
N
391
N
C
N
392
N
O
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
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
sing
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
doub
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
Y
329
N
doub
Y
330
N
sing
Y
331
N
sing
N
332
N
sing
Y
333
N
doub
Y
334
N
sing
Y
335
N
sing
N
336
N
sing
Y
337
N
sing
Y
338
N
doub
N
339
N
sing
Y
340
N
doub
N
341
N
sing
Y
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
sing
N
351
N
sing
N
352
N
doub
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
Y
357
N
doub
Y
358
N
sing
Y
359
N
sing
N
360
N
sing
Y
361
N
doub
N
362
N
sing
Y
363
N
doub
N
364
N
sing
Y
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
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
To be Published
0353
Crystal structure of Staphylococcal nuclease variant PHS T62K at cryogenic temperature
10.2210/pdb3dmu/pdb
pdb_00003dmu
100
1
multi-layer optics
CCD
2005-01-20
BRUKER APEX II
GE111
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
SEALED TUBE
OTHER
16790.354
Thermonuclease
3.1.31.1
T62K/P117G/H124L/S128A
1
man
polymer
94.971
PHOSPHATE ION
1
syn
non-polymer
118.174
(4S)-2-METHYL-2,4-PENTANEDIOL
1
syn
non-polymer
18.015
water
73
nat
water
TNase, Micrococcal nuclease, Staphylococcal nuclease, Nuclease B, Nuclease A
no
no
ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFKKKMVENAKKIEVEFDKGQ
RTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKGNNTHEQLLRKAEAQAKKEKLNIWSEDNADSGQ
ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFKKKMVENAKKIEVEFDKGQ
RTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKGNNTHEQLLRKAEAQAKKEKLNIWSEDNADSGQ
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
Escherichia coli
BL21(DE3)
plasmid
pET24a+
1
2.19
43.86
VAPOR DIFFUSION, HANGING DROP
8.0
44% MPD, 25 mM Potassium Phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
277
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
2008-11-04
1
1
2011-07-13
1
2
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
STRUCTURE OF S. NUCLEASE STABILIZING TRIPLE MUTANT P117G/H124L/S128A
THE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE REFINED AT 1.7 ANGSTROMS RESOLUTION
RCSB
Y
RCSB
2008-07-01
REL
REL
PO4
PHOSPHATE ION
MPD
(4S)-2-METHYL-2,4-PENTANEDIOL
HOH
water
1EY8
1EY8.PDB
PDB
experimental model
PO4
1
2
PO4
PO4
150
A
MPD
1
3
MPD
MPD
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
26
4
HOH
HOH
176
A
HOH
27
4
HOH
HOH
177
A
HOH
28
4
HOH
HOH
178
A
HOH
29
4
HOH
HOH
179
A
HOH
30
4
HOH
HOH
180
A
HOH
31
4
HOH
HOH
181
A
HOH
32
4
HOH
HOH
182
A
HOH
33
4
HOH
HOH
183
A
HOH
34
4
HOH
HOH
184
A
HOH
35
4
HOH
HOH
185
A
HOH
36
4
HOH
HOH
186
A
HOH
37
4
HOH
HOH
187
A
HOH
38
4
HOH
HOH
188
A
HOH
39
4
HOH
HOH
189
A
HOH
40
4
HOH
HOH
190
A
HOH
41
4
HOH
HOH
191
A
HOH
42
4
HOH
HOH
192
A
HOH
43
4
HOH
HOH
193
A
HOH
44
4
HOH
HOH
194
A
HOH
45
4
HOH
HOH
195
A
HOH
46
4
HOH
HOH
196
A
HOH
47
4
HOH
HOH
197
A
HOH
48
4
HOH
HOH
198
A
HOH
49
4
HOH
HOH
199
A
HOH
50
4
HOH
HOH
200
A
HOH
51
4
HOH
HOH
201
A
HOH
54
4
HOH
HOH
202
A
HOH
55
4
HOH
HOH
203
A
HOH
56
4
HOH
HOH
204
A
HOH
57
4
HOH
HOH
205
A
HOH
58
4
HOH
HOH
206
A
HOH
60
4
HOH
HOH
207
A
HOH
61
4
HOH
HOH
208
A
HOH
62
4
HOH
HOH
209
A
HOH
64
4
HOH
HOH
210
A
HOH
65
4
HOH
HOH
211
A
HOH
66
4
HOH
HOH
212
A
HOH
67
4
HOH
HOH
213
A
HOH
68
4
HOH
HOH
214
A
HOH
70
4
HOH
HOH
215
A
HOH
71
4
HOH
HOH
216
A
HOH
72
4
HOH
HOH
217
A
HOH
73
4
HOH
HOH
218
A
HOH
74
4
HOH
HOH
219
A
HOH
77
4
HOH
HOH
220
A
HOH
79
4
HOH
HOH
221
A
HOH
80
4
HOH
HOH
222
A
HOH
81
4
HOH
HOH
223
A
HOH
82
4
HOH
HOH
224
A
2.500
2.500
17.940
17.940
Phaser MODE: MR_AUTO
Solvent flattening and Histogram matching
13486
35.300
0.796
505
28.200
0.899
507
27.400
0.910
507
27.000
0.908
505
29.100
0.889
508
32.700
0.891
502
33.600
0.873
514
35.100
0.848
501
35.500
0.851
509
34.600
0.872
504
35.500
0.861
516
34.700
0.848
522
38.200
0.837
533
37.100
0.846
553
38.000
0.838
565
37.800
0.828
558
37.000
0.844
605
40.800
0.794
594
41.500
0.819
626
39.400
0.750
620
42.200
0.770
648
49.200
0.742
639
49.600
0.692
681
50.300
0.666
764
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
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
LYS
53
n
53
LYS
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
LYS
62
n
62
LYS
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
GLY
117
n
117
GLY
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
LEU
124
n
124
LEU
124
A
LEU
125
n
125
LEU
125
A
ARG
126
n
126
ARG
126
A
LYS
127
n
127
LYS
127
A
ALA
128
n
128
ALA
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
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
TYR
27
A
N
TYR
27
A
O
GLN
30
A
O
GLN
30
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
LYS
6
A
LYS
6
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
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
ASN
138
47.46
-112.69
27.909
0.000
0.000
0.000
0.000
0.000
0.000
0.954
0.926
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.255
0.198
0.230
0.203
1.800
17.00
1272
13483
12753
10.000
94.610
3.133
0.099
RANDOM
1
THROUGHOUT
0.00
0.00
MOLECULAR REPLACEMENT
0.150
0.151
0.800
0.800
1.200
1EY8.PDB
MAXIMUM LIKELIHOOD
MASK
1.800
17.00
81
1110
5
0
1024
0.009
0.022
1061
2.080
1.998
1428
7.470
5.000
134
29.248
24.773
44
18.093
15.000
217
20.903
15.000
5
0.157
0.200
156
0.005
0.021
760
2.056
1.500
638
3.159
2.000
1024
5.070
3.000
423
7.239
4.500
399
0.383
0.251
1.846
98
749
847
1091
20
85.300
0.310
0.232
1.896
66
1030
20
87.241
0.255
0.198
1.950
94
1027
20
89.496
0.327
0.218
2.010
83
979
20
91.183
0.299
0.215
2.075
78
949
20
93.915
0.284
0.206
2.146
76
934
20
94.639
33.1
1.75
17.98
3DMU
14741
14710
0
0
0.0301
0.0199
1
30.16
10.6
99.8
0.2839
1.75
1.84
4.05
2016
0.2574
3.43
99.3
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
phasing
K. Cowtan
ccp4@dl.ac.uk
Fortran_77
http://www.ccp4.ac.uk/main.html
DM
program
6.0.99d
refinement
Murshudov, G.N.
ccp4@dl.ac.uk
Fortran_77
http://www.ccp4.ac.uk/main.html
REFMAC
program
5.5.0017
data extraction
PDB
sw-help@rcsb.rutgers.edu
September 10, 2007
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
3.005
data collection
APEX
data reduction
SAINT
Crystal structure of Staphylococcal nuclease variant PHS T62K at cryogenic temperature
1
N
N
2
N
N
3
N
N
4
N
N
A
TYR
54
A
TYR
54
HELX_P
A
ALA
69
A
ALA
69
1
1
16
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
HYDROLASE
Staphylococcal nuclease, hyperstable variant, hydrolase, pdtp, Calcium, Endonuclease, Membrane, Metal-binding, Nuclease, Secreted, Zymogen
NUC_STAAU
UNP
1
83
P00644
ATSTKKLHKEPATLIKAIDGDTVKLMYKGQPMTFRLLLVDTPETKHPKKGVEKYGPEASAFTKKMVENAKKIEVEFDKGQ
RTDKYGRGLAYIYADGKMVNEALVRQGLAKVAYVYKPNNTHEQHLRKSEAQAKKEKLNIWSEDNADSGQ
83
231
3DMU
1
149
P00644
A
1
1
149
1
THR
expression tag
LYS
62
3DMU
A
P00644
UNP
144
62
1
PRO
expression tag
GLY
117
3DMU
A
P00644
UNP
199
117
1
HIS
expression tag
LEU
124
3DMU
A
P00644
UNP
206
124
1
SER
expression tag
ALA
128
3DMU
A
P00644
UNP
210
128
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
PHE
76
A
PHE
76
A
GLU
10
A
GLU
10
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
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 PO4 A 150
A
PO4
150
Software
4
BINDING SITE FOR RESIDUE MPD A 151
A
MPD
151
Software
5
A
TYR
27
A
TYR
27
4
1_555
A
LYS
28
A
LYS
28
4
1_555
A
LYS
134
A
LYS
134
4
2_565
A
LYS
136
A
LYS
136
4
2_565
A
ASP
21
A
ASP
21
5
1_555
A
ARG
35
A
ARG
35
5
1_555
A
LYS
70
A
LYS
70
5
3_555
A
LYS
71
A
LYS
71
5
3_555
A
ARG
87
A
ARG
87
5
1_555
76
P 41