0.020360
0.000000
0.000188
0.000000
0.024938
0.000000
0.000000
0.000000
0.019752
0.00000
0.00000
0.00000
Yuan, H.S.
Li, C.L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.00
90.53
90.00
49.115
40.099
50.631
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
Mg 2
24.305
MAGNESIUM ION
non-polymer
C5 H11 N O2 Se
196.106
n
SELENOMETHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
UK
Embo J.
EMJODG
0897
0261-4189
22
4014
4025
10.1093/emboj/cdg377
12881435
DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site.
2003
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2001-12-16
ADSC QUANTUM 4
SI 111 + GE 220
MAD
M
x-ray
1
0.9795
1.0
0.9796
1.0
0.9600
1.0
BL-18B
Photon Factory
0.9795, 0.9796, 0.9600
SYNCHROTRON
PHOTON FACTORY BEAMLINE BL-18B
24695.891
Nuclease
3.1.-.-
residue 19-228
1
man
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
18.015
water
194
nat
water
VVN Nuclease
no
yes
APPSSFSAAKQQAVKIYQDHPISFYCGCDIEWQGKKGIPNLETCGYQVRKQQTRASRIEWEHVVPAWQFGHHRQCWQKGG
RKNCSKNDQQFRL(MSE)EADLHNLTPAIGEVNGDRSNFNFSQWNGVDGVSYGRCE(MSE)QVNFKQRKV(MSE)PPDRA
RGSIARTYLY(MSE)SQEYGFQLSKQQQQL(MSE)QAWNKSYPVDEWECTRDDRIAKIQGNHNPFVQQSC
APPSSFSAAKQQAVKIYQDHPISFYCGCDIEWQGKKGIPNLETCGYQVRKQQTRASRIEWEHVVPAWQFGHHRQCWQKGG
RKNCSKNDQQFRLMEADLHNLTPAIGEVNGDRSNFNFSQWNGVDGVSYGRCEMQVNFKQRKVMPPDRARGSIARTYLYMS
QEYGFQLSKQQQQLMQAWNKSYPVDEWECTRDDRIAKIQGNHNPFVQQSC
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Vibrio
Escherichia
sample
672
Vibrio vulnificus
562
Escherichia coli
B834(DE3)
plasmid
pTYB2
1
1.79
30.61
VAPOR DIFFUSION, HANGING DROP
6.5
PEG8000, ammonium acetate, magnesium acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
repository
Initial release
Version format compliance
Version format compliance
1
0
2003-08-05
1
1
2008-04-29
1
2
2011-07-13
1OUP contains the same protein complexed with DNA
RCSB
Y
PDBJ
2003-03-25
REL
REL
MG
MAGNESIUM ION
HOH
water
MG
494
2
MG
MG
494
A
TIP
300
3
HOH
HOH
300
A
TIP
301
3
HOH
HOH
301
A
TIP
302
3
HOH
HOH
302
A
TIP
303
3
HOH
HOH
303
A
TIP
304
3
HOH
HOH
304
A
TIP
305
3
HOH
HOH
305
A
TIP
306
3
HOH
HOH
306
A
TIP
307
3
HOH
HOH
307
A
TIP
308
3
HOH
HOH
308
A
TIP
309
3
HOH
HOH
309
A
TIP
310
3
HOH
HOH
310
A
TIP
311
3
HOH
HOH
311
A
TIP
312
3
HOH
HOH
312
A
TIP
313
3
HOH
HOH
313
A
TIP
314
3
HOH
HOH
314
A
TIP
315
3
HOH
HOH
315
A
TIP
316
3
HOH
HOH
316
A
TIP
317
3
HOH
HOH
317
A
TIP
318
3
HOH
HOH
318
A
TIP
319
3
HOH
HOH
319
A
TIP
320
3
HOH
HOH
320
A
TIP
321
3
HOH
HOH
321
A
TIP
322
3
HOH
HOH
322
A
TIP
323
3
HOH
HOH
323
A
TIP
324
3
HOH
HOH
324
A
TIP
325
3
HOH
HOH
325
A
TIP
326
3
HOH
HOH
326
A
TIP
327
3
HOH
HOH
327
A
TIP
328
3
HOH
HOH
328
A
TIP
329
3
HOH
HOH
329
A
TIP
330
3
HOH
HOH
330
A
TIP
331
3
HOH
HOH
331
A
TIP
332
3
HOH
HOH
332
A
TIP
333
3
HOH
HOH
333
A
TIP
334
3
HOH
HOH
334
A
TIP
335
3
HOH
HOH
335
A
TIP
336
3
HOH
HOH
336
A
TIP
337
3
HOH
HOH
337
A
TIP
338
3
HOH
HOH
338
A
TIP
339
3
HOH
HOH
339
A
TIP
340
3
HOH
HOH
340
A
TIP
341
3
HOH
HOH
341
A
TIP
342
3
HOH
HOH
342
A
TIP
343
3
HOH
HOH
343
A
TIP
344
3
HOH
HOH
344
A
TIP
345
3
HOH
HOH
345
A
TIP
346
3
HOH
HOH
346
A
TIP
347
3
HOH
HOH
347
A
TIP
348
3
HOH
HOH
348
A
TIP
349
3
HOH
HOH
349
A
TIP
350
3
HOH
HOH
350
A
TIP
351
3
HOH
HOH
351
A
TIP
352
3
HOH
HOH
352
A
TIP
353
3
HOH
HOH
353
A
TIP
354
3
HOH
HOH
354
A
TIP
355
3
HOH
HOH
355
A
TIP
356
3
HOH
HOH
356
A
TIP
357
3
HOH
HOH
357
A
TIP
358
3
HOH
HOH
358
A
TIP
359
3
HOH
HOH
359
A
TIP
360
3
HOH
HOH
360
A
TIP
361
3
HOH
HOH
361
A
TIP
362
3
HOH
HOH
362
A
TIP
363
3
HOH
HOH
363
A
TIP
364
3
HOH
HOH
364
A
TIP
365
3
HOH
HOH
365
A
TIP
366
3
HOH
HOH
366
A
TIP
367
3
HOH
HOH
367
A
TIP
368
3
HOH
HOH
368
A
TIP
369
3
HOH
HOH
369
A
TIP
370
3
HOH
HOH
370
A
TIP
371
3
HOH
HOH
371
A
TIP
372
3
HOH
HOH
372
A
TIP
373
3
HOH
HOH
373
A
TIP
374
3
HOH
HOH
374
A
TIP
375
3
HOH
HOH
375
A
TIP
376
3
HOH
HOH
376
A
TIP
377
3
HOH
HOH
377
A
TIP
378
3
HOH
HOH
378
A
TIP
379
3
HOH
HOH
379
A
TIP
380
3
HOH
HOH
380
A
TIP
381
3
HOH
HOH
381
A
TIP
382
3
HOH
HOH
382
A
TIP
383
3
HOH
HOH
383
A
TIP
384
3
HOH
HOH
384
A
TIP
385
3
HOH
HOH
385
A
TIP
386
3
HOH
HOH
386
A
TIP
387
3
HOH
HOH
387
A
TIP
388
3
HOH
HOH
388
A
TIP
389
3
HOH
HOH
389
A
TIP
390
3
HOH
HOH
390
A
TIP
391
3
HOH
HOH
391
A
TIP
392
3
HOH
HOH
392
A
TIP
393
3
HOH
HOH
393
A
TIP
394
3
HOH
HOH
394
A
TIP
395
3
HOH
HOH
395
A
TIP
396
3
HOH
HOH
396
A
TIP
397
3
HOH
HOH
397
A
TIP
398
3
HOH
HOH
398
A
TIP
399
3
HOH
HOH
399
A
TIP
400
3
HOH
HOH
400
A
TIP
401
3
HOH
HOH
401
A
TIP
402
3
HOH
HOH
402
A
TIP
403
3
HOH
HOH
403
A
TIP
404
3
HOH
HOH
404
A
TIP
405
3
HOH
HOH
405
A
TIP
406
3
HOH
HOH
406
A
TIP
407
3
HOH
HOH
407
A
TIP
408
3
HOH
HOH
408
A
TIP
409
3
HOH
HOH
409
A
TIP
410
3
HOH
HOH
410
A
TIP
411
3
HOH
HOH
411
A
TIP
412
3
HOH
HOH
412
A
TIP
413
3
HOH
HOH
413
A
TIP
414
3
HOH
HOH
414
A
TIP
415
3
HOH
HOH
415
A
TIP
416
3
HOH
HOH
416
A
TIP
417
3
HOH
HOH
417
A
TIP
418
3
HOH
HOH
418
A
TIP
419
3
HOH
HOH
419
A
TIP
420
3
HOH
HOH
420
A
TIP
421
3
HOH
HOH
421
A
TIP
422
3
HOH
HOH
422
A
TIP
423
3
HOH
HOH
423
A
TIP
424
3
HOH
HOH
424
A
TIP
425
3
HOH
HOH
425
A
TIP
426
3
HOH
HOH
426
A
TIP
427
3
HOH
HOH
427
A
TIP
428
3
HOH
HOH
428
A
TIP
429
3
HOH
HOH
429
A
TIP
430
3
HOH
HOH
430
A
TIP
431
3
HOH
HOH
431
A
TIP
432
3
HOH
HOH
432
A
TIP
433
3
HOH
HOH
433
A
TIP
434
3
HOH
HOH
434
A
TIP
435
3
HOH
HOH
435
A
TIP
436
3
HOH
HOH
436
A
TIP
437
3
HOH
HOH
437
A
TIP
438
3
HOH
HOH
438
A
TIP
439
3
HOH
HOH
439
A
TIP
440
3
HOH
HOH
440
A
TIP
441
3
HOH
HOH
441
A
TIP
442
3
HOH
HOH
442
A
TIP
443
3
HOH
HOH
443
A
TIP
444
3
HOH
HOH
444
A
TIP
445
3
HOH
HOH
445
A
TIP
446
3
HOH
HOH
446
A
TIP
447
3
HOH
HOH
447
A
TIP
448
3
HOH
HOH
448
A
TIP
449
3
HOH
HOH
449
A
TIP
450
3
HOH
HOH
450
A
TIP
451
3
HOH
HOH
451
A
TIP
452
3
HOH
HOH
452
A
TIP
453
3
HOH
HOH
453
A
TIP
454
3
HOH
HOH
454
A
TIP
455
3
HOH
HOH
455
A
TIP
456
3
HOH
HOH
456
A
TIP
457
3
HOH
HOH
457
A
TIP
458
3
HOH
HOH
458
A
TIP
459
3
HOH
HOH
459
A
TIP
460
3
HOH
HOH
460
A
TIP
461
3
HOH
HOH
461
A
TIP
462
3
HOH
HOH
462
A
TIP
463
3
HOH
HOH
463
A
TIP
464
3
HOH
HOH
464
A
TIP
465
3
HOH
HOH
465
A
TIP
466
3
HOH
HOH
466
A
TIP
467
3
HOH
HOH
467
A
TIP
468
3
HOH
HOH
468
A
TIP
469
3
HOH
HOH
469
A
TIP
470
3
HOH
HOH
470
A
TIP
471
3
HOH
HOH
471
A
TIP
472
3
HOH
HOH
472
A
TIP
473
3
HOH
HOH
473
A
TIP
474
3
HOH
HOH
474
A
TIP
475
3
HOH
HOH
475
A
TIP
476
3
HOH
HOH
476
A
TIP
477
3
HOH
HOH
477
A
TIP
478
3
HOH
HOH
478
A
TIP
479
3
HOH
HOH
479
A
TIP
480
3
HOH
HOH
480
A
TIP
481
3
HOH
HOH
481
A
TIP
482
3
HOH
HOH
482
A
TIP
483
3
HOH
HOH
483
A
TIP
484
3
HOH
HOH
484
A
TIP
485
3
HOH
HOH
485
A
TIP
486
3
HOH
HOH
486
A
TIP
487
3
HOH
HOH
487
A
TIP
488
3
HOH
HOH
488
A
TIP
489
3
HOH
HOH
489
A
TIP
490
3
HOH
HOH
490
A
TIP
491
3
HOH
HOH
491
A
TIP
492
3
HOH
HOH
492
A
TIP
493
3
HOH
HOH
493
A
ALA
19
n
1
ALA
19
A
PRO
20
n
2
PRO
20
A
PRO
21
n
3
PRO
21
A
SER
22
n
4
SER
22
A
SER
23
n
5
SER
23
A
PHE
24
n
6
PHE
24
A
SER
25
n
7
SER
25
A
ALA
26
n
8
ALA
26
A
ALA
27
n
9
ALA
27
A
LYS
28
n
10
LYS
28
A
GLN
29
n
11
GLN
29
A
GLN
30
n
12
GLN
30
A
ALA
31
n
13
ALA
31
A
VAL
32
n
14
VAL
32
A
LYS
33
n
15
LYS
33
A
ILE
34
n
16
ILE
34
A
TYR
35
n
17
TYR
35
A
GLN
36
n
18
GLN
36
A
ASP
37
n
19
ASP
37
A
HIS
38
n
20
HIS
38
A
PRO
39
n
21
PRO
39
A
ILE
40
n
22
ILE
40
A
SER
41
n
23
SER
41
A
PHE
42
n
24
PHE
42
A
TYR
43
n
25
TYR
43
A
CYS
44
n
26
CYS
44
A
GLY
45
n
27
GLY
45
A
CYS
46
n
28
CYS
46
A
ASP
47
n
29
ASP
47
A
ILE
48
n
30
ILE
48
A
GLU
49
n
31
GLU
49
A
TRP
50
n
32
TRP
50
A
GLN
51
n
33
GLN
51
A
GLY
52
n
34
GLY
52
A
LYS
53
n
35
LYS
53
A
LYS
54
n
36
LYS
54
A
GLY
55
n
37
GLY
55
A
ILE
56
n
38
ILE
56
A
PRO
57
n
39
PRO
57
A
ASN
58
n
40
ASN
58
A
LEU
59
n
41
LEU
59
A
GLU
60
n
42
GLU
60
A
THR
61
n
43
THR
61
A
CYS
62
n
44
CYS
62
A
GLY
63
n
45
GLY
63
A
TYR
64
n
46
TYR
64
A
GLN
65
n
47
GLN
65
A
VAL
66
n
48
VAL
66
A
ARG
67
n
49
ARG
67
A
LYS
68
n
50
LYS
68
A
GLN
69
n
51
GLN
69
A
GLN
70
n
52
GLN
70
A
THR
71
n
53
THR
71
A
ARG
72
n
54
ARG
72
A
ALA
73
n
55
ALA
73
A
SER
74
n
56
SER
74
A
ARG
75
n
57
ARG
75
A
ILE
76
n
58
ILE
76
A
GLU
77
n
59
GLU
77
A
TRP
78
n
60
TRP
78
A
GLU
79
n
61
GLU
79
A
HIS
80
n
62
HIS
80
A
VAL
81
n
63
VAL
81
A
VAL
82
n
64
VAL
82
A
PRO
83
n
65
PRO
83
A
ALA
84
n
66
ALA
84
A
TRP
85
n
67
TRP
85
A
GLN
86
n
68
GLN
86
A
PHE
87
n
69
PHE
87
A
GLY
88
n
70
GLY
88
A
HIS
89
n
71
HIS
89
A
HIS
90
n
72
HIS
90
A
ARG
91
n
73
ARG
91
A
GLN
92
n
74
GLN
92
A
CYS
93
n
75
CYS
93
A
TRP
94
n
76
TRP
94
A
GLN
95
n
77
GLN
95
A
LYS
96
n
78
LYS
96
A
GLY
97
n
79
GLY
97
A
GLY
98
n
80
GLY
98
A
ARG
99
n
81
ARG
99
A
LYS
100
n
82
LYS
100
A
ASN
101
n
83
ASN
101
A
CYS
102
n
84
CYS
102
A
SER
103
n
85
SER
103
A
LYS
104
n
86
LYS
104
A
ASN
105
n
87
ASN
105
A
ASP
106
n
88
ASP
106
A
GLN
107
n
89
GLN
107
A
GLN
108
n
90
GLN
108
A
PHE
109
n
91
PHE
109
A
ARG
110
n
92
ARG
110
A
LEU
111
n
93
LEU
111
A
MSE
112
n
94
MSE
112
A
GLU
113
n
95
GLU
113
A
ALA
114
n
96
ALA
114
A
ASP
115
n
97
ASP
115
A
LEU
116
n
98
LEU
116
A
HIS
117
n
99
HIS
117
A
ASN
118
n
100
ASN
118
A
LEU
119
n
101
LEU
119
A
THR
120
n
102
THR
120
A
PRO
121
n
103
PRO
121
A
ALA
122
n
104
ALA
122
A
ILE
123
n
105
ILE
123
A
GLY
124
n
106
GLY
124
A
GLU
125
n
107
GLU
125
A
VAL
126
n
108
VAL
126
A
ASN
127
n
109
ASN
127
A
GLY
128
n
110
GLY
128
A
ASP
129
n
111
ASP
129
A
ARG
130
n
112
ARG
130
A
SER
131
n
113
SER
131
A
ASN
132
n
114
ASN
132
A
PHE
133
n
115
PHE
133
A
ASN
134
n
116
ASN
134
A
PHE
135
n
117
PHE
135
A
SER
136
n
118
SER
136
A
GLN
137
n
119
GLN
137
A
TRP
138
n
120
TRP
138
A
ASN
139
n
121
ASN
139
A
GLY
140
n
122
GLY
140
A
VAL
141
n
123
VAL
141
A
ASP
142
n
124
ASP
142
A
GLY
143
n
125
GLY
143
A
VAL
144
n
126
VAL
144
A
SER
145
n
127
SER
145
A
TYR
146
n
128
TYR
146
A
GLY
147
n
129
GLY
147
A
ARG
148
n
130
ARG
148
A
CYS
149
n
131
CYS
149
A
GLU
150
n
132
GLU
150
A
MSE
151
n
133
MSE
151
A
GLN
152
n
134
GLN
152
A
VAL
153
n
135
VAL
153
A
ASN
154
n
136
ASN
154
A
PHE
155
n
137
PHE
155
A
LYS
156
n
138
LYS
156
A
GLN
157
n
139
GLN
157
A
ARG
158
n
140
ARG
158
A
LYS
159
n
141
LYS
159
A
VAL
160
n
142
VAL
160
A
MSE
161
n
143
MSE
161
A
PRO
162
n
144
PRO
162
A
PRO
163
n
145
PRO
163
A
ASP
164
n
146
ASP
164
A
ARG
165
n
147
ARG
165
A
ALA
166
n
148
ALA
166
A
ARG
167
n
149
ARG
167
A
GLY
168
n
150
GLY
168
A
SER
169
n
151
SER
169
A
ILE
170
n
152
ILE
170
A
ALA
171
n
153
ALA
171
A
ARG
172
n
154
ARG
172
A
THR
173
n
155
THR
173
A
TYR
174
n
156
TYR
174
A
LEU
175
n
157
LEU
175
A
TYR
176
n
158
TYR
176
A
MSE
177
n
159
MSE
177
A
SER
178
n
160
SER
178
A
GLN
179
n
161
GLN
179
A
GLU
180
n
162
GLU
180
A
TYR
181
n
163
TYR
181
A
GLY
182
n
164
GLY
182
A
PHE
183
n
165
PHE
183
A
GLN
184
n
166
GLN
184
A
LEU
185
n
167
LEU
185
A
SER
186
n
168
SER
186
A
LYS
187
n
169
LYS
187
A
GLN
188
n
170
GLN
188
A
GLN
189
n
171
GLN
189
A
GLN
190
n
172
GLN
190
A
GLN
191
n
173
GLN
191
A
LEU
192
n
174
LEU
192
A
MSE
193
n
175
MSE
193
A
GLN
194
n
176
GLN
194
A
ALA
195
n
177
ALA
195
A
TRP
196
n
178
TRP
196
A
ASN
197
n
179
ASN
197
A
LYS
198
n
180
LYS
198
A
SER
199
n
181
SER
199
A
TYR
200
n
182
TYR
200
A
PRO
201
n
183
PRO
201
A
VAL
202
n
184
VAL
202
A
ASP
203
n
185
ASP
203
A
GLU
204
n
186
GLU
204
A
TRP
205
n
187
TRP
205
A
GLU
206
n
188
GLU
206
A
CYS
207
n
189
CYS
207
A
THR
208
n
190
THR
208
A
ARG
209
n
191
ARG
209
A
ASP
210
n
192
ASP
210
A
ASP
211
n
193
ASP
211
A
ARG
212
n
194
ARG
212
A
ILE
213
n
195
ILE
213
A
ALA
214
n
196
ALA
214
A
LYS
215
n
197
LYS
215
A
ILE
216
n
198
ILE
216
A
GLN
217
n
199
GLN
217
A
GLY
218
n
200
GLY
218
A
ASN
219
n
201
ASN
219
A
HIS
220
n
202
HIS
220
A
ASN
221
n
203
ASN
221
A
PRO
222
n
204
PRO
222
A
PHE
223
n
205
PHE
223
A
VAL
224
n
206
VAL
224
A
GLN
225
n
207
GLN
225
A
GLN
226
n
208
GLN
226
A
SER
227
n
209
SER
227
A
CYS
228
n
210
CYS
228
A
author_defined_assembly
1
monomeric
A
GLU
79
A
OE1
GLU
61
1_555
A
MG
494
B
MG
MG
1_555
A
ASN
127
A
OD1
ASN
109
1_555
86.4
A
GLU
79
A
OE1
GLU
61
1_555
A
MG
494
B
MG
MG
1_555
A
HOH
323
C
O
HOH
1_555
96.1
A
ASN
127
A
OD1
ASN
109
1_555
A
MG
494
B
MG
MG
1_555
A
HOH
323
C
O
HOH
1_555
169.1
A
GLU
79
A
OE1
GLU
61
1_555
A
MG
494
B
MG
MG
1_555
A
HOH
336
C
O
HOH
1_555
172.2
A
ASN
127
A
OD1
ASN
109
1_555
A
MG
494
B
MG
MG
1_555
A
HOH
336
C
O
HOH
1_555
101.4
A
HOH
323
C
O
HOH
1_555
A
MG
494
B
MG
MG
1_555
A
HOH
336
C
O
HOH
1_555
76.1
A
GLU
79
A
OE1
GLU
61
1_555
A
MG
494
B
MG
MG
1_555
A
HOH
493
C
O
HOH
1_555
85.5
A
ASN
127
A
OD1
ASN
109
1_555
A
MG
494
B
MG
MG
1_555
A
HOH
493
C
O
HOH
1_555
86.7
A
HOH
323
C
O
HOH
1_555
A
MG
494
B
MG
MG
1_555
A
HOH
493
C
O
HOH
1_555
83.0
A
HOH
336
C
O
HOH
1_555
A
MG
494
B
MG
MG
1_555
A
HOH
493
C
O
HOH
1_555
94.5
A
GLU
79
A
OE1
GLU
61
1_555
A
MG
494
B
MG
MG
1_555
A
HOH
492
C
O
HOH
1_555
109.3
A
ASN
127
A
OD1
ASN
109
1_555
A
MG
494
B
MG
MG
1_555
A
HOH
492
C
O
HOH
1_555
99.0
A
HOH
323
C
O
HOH
1_555
A
MG
494
B
MG
MG
1_555
A
HOH
492
C
O
HOH
1_555
90.3
A
HOH
336
C
O
HOH
1_555
A
MG
494
B
MG
MG
1_555
A
HOH
492
C
O
HOH
1_555
70.1
A
HOH
493
C
O
HOH
1_555
A
MG
494
B
MG
MG
1_555
A
HOH
492
C
O
HOH
1_555
164.4
A
MSE
112
SELENOMETHIONINE
A
MSE
94
MET
A
MSE
151
SELENOMETHIONINE
A
MSE
133
MET
A
MSE
161
SELENOMETHIONINE
A
MSE
143
MET
A
MSE
177
SELENOMETHIONINE
A
MSE
159
MET
A
MSE
193
SELENOMETHIONINE
A
MSE
175
MET
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
N
GLN
51
A
N
GLN
33
A
O
LYS
54
A
O
LYS
36
A
N
GLU
79
A
N
GLU
61
A
O
THR
120
A
O
THR
102
A
N
ASN
134
A
N
ASN
116
A
O
VAL
160
A
O
VAL
142
A
O
MSE
161
A
O
MSE
143
A
N
GLN
152
A
N
GLN
134
A
O
VAL
153
A
O
VAL
135
A
N
VAL
144
A
N
VAL
126
1
A
A
SE
CE
MSE
MSE
161
161
-0.392
0.059
1.950
1.558
N
1
A
PRO
21
-48.41
154.12
1
A
LYS
68
-166.28
-21.80
1
A
SER
131
54.24
-125.75
1
A
ASP
142
-152.62
43.69
PROTEIN_REP.PARAM
PROTEIN.TOP
WATER_REP.PARAM
WATER.TOP
ION.PARAM
ION.TOP
24.3
-6.33
0.00
4.57
-3.15
0.00
9.48
0.269
0.010
0.186
2.30
26.55
713
16490
8803
8.3
98.4
RANDOM
283277.67
0.000
1
RESTRAINED
THROUGHOUT
0
MAD
Engh & Huber
FLAT MODEL
48.3607
0.348624
0.36
0.22
5.00
0.24
0.15
2.30
26.55
194
1913
1
0
1718
0.012
1.3
22.4
0.80
1.32
1.50
1.93
2.00
2.25
2.00
3.06
2.50
0.262
0.023
0.185
2.44
133
1275
2424
6
9.4
95.8
15.6
2.3
40
1OUO
9512
9127
0
0
0.075
1
24.38
6.822
96
2.3
2.38
9.57
0.146
96
refinement
CNS
1.0
data reduction
DENZO
data scaling
SCALEPACK
phasing
CNS
Nuclease (E.C.3.1.-.-)
Crystal structure of the periplasmic endonuclease Vvn
1
N
N
2
N
N
3
N
N
A
SER
23
A
SER
5
HELX_P
A
TYR
35
A
TYR
17
1
1
13
A
GLN
69
A
GLN
51
HELX_P
A
SER
74
A
SER
56
1
2
6
A
ARG
91
A
ARG
73
HELX_P
A
ASP
106
A
ASP
88
1
3
16
A
ASP
106
A
ASP
88
HELX_P
A
ASP
115
A
ASP
97
1
4
10
A
GLY
124
A
GLY
106
HELX_P
A
SER
131
A
SER
113
1
5
8
A
PRO
163
A
PRO
145
HELX_P
A
TYR
181
A
TYR
163
1
6
19
A
SER
186
A
SER
168
HELX_P
A
TYR
200
A
TYR
182
1
7
15
A
ASP
203
A
ASP
185
HELX_P
A
GLY
218
A
GLY
200
1
8
16
A
ASN
221
A
ASN
203
HELX_P
A
GLN
226
A
GLN
208
1
9
6
disulf
2.041
A
CYS
44
A
SG
CYS
26
1_555
A
CYS
149
A
SG
CYS
131
1_555
disulf
2.024
A
CYS
46
A
SG
CYS
28
1_555
A
CYS
62
A
SG
CYS
44
1_555
disulf
2.036
A
CYS
93
A
SG
CYS
75
1_555
A
CYS
102
A
SG
CYS
84
1_555
disulf
2.035
A
CYS
207
A
SG
CYS
189
1_555
A
CYS
228
A
SG
CYS
210
1_555
metalc
1.806
A
MG
494
B
MG
MG
1_555
A
GLU
79
A
OE1
GLU
61
1_555
metalc
1.986
A
MG
494
B
MG
MG
1_555
A
ASN
127
A
OD1
ASN
109
1_555
covale
1.333
A
LEU
111
A
C
LEU
93
1_555
A
MSE
112
A
N
MSE
94
1_555
covale
1.322
A
MSE
112
A
C
MSE
94
1_555
A
GLU
113
A
N
GLU
95
1_555
covale
1.331
A
GLU
150
A
C
GLU
132
1_555
A
MSE
151
A
N
MSE
133
1_555
covale
1.327
A
MSE
151
A
C
MSE
133
1_555
A
GLN
152
A
N
GLN
134
1_555
covale
1.322
A
VAL
160
A
C
VAL
142
1_555
A
MSE
161
A
N
MSE
143
1_555
covale
1.340
A
MSE
161
A
C
MSE
143
1_555
A
PRO
162
A
N
PRO
144
1_555
covale
1.330
A
TYR
176
A
C
TYR
158
1_555
A
MSE
177
A
N
MSE
159
1_555
covale
1.327
A
MSE
177
A
C
MSE
159
1_555
A
SER
178
A
N
SER
160
1_555
covale
1.328
A
LEU
192
A
C
LEU
174
1_555
A
MSE
193
A
N
MSE
175
1_555
covale
1.331
A
MSE
193
A
C
MSE
175
1_555
A
GLN
194
A
N
GLN
176
1_555
metalc
2.289
A
MG
494
B
MG
MG
1_555
A
HOH
323
C
O
HOH
1_555
metalc
2.344
A
MG
494
B
MG
MG
1_555
A
HOH
336
C
O
HOH
1_555
metalc
1.876
A
MG
494
B
MG
MG
1_555
A
HOH
493
C
O
HOH
1_555
metalc
2.215
A
MG
494
B
MG
MG
1_555
A
HOH
492
C
O
HOH
1_555
HYDROLASE
Non-specific endonuclease, beta-beta-alpha-metal motif, HYDROLASE
Q8DCA6_VIBVU
UNP
1
19
Q8DCA6
APPSSFSAAKQQAVKIYQDHPISFYCGCDIEWQGKKGIPNLETCGYQVRKQQTRASRIEWEHVVPAWQFGHHRQCWQKGG
RKNCSKNDQQFRLMEADLHNLTPAIGEVNGDRSNFNFSQWNGVDGVSYGRCEMQVNFKQRKVMPQTELRGSIARTYLYMS
QEYGFQLSKQQQQLMQAWNKSYPVDEWECTRDDRIAKIQGNHNPFVQQSC
19
228
1OUO
19
228
Q8DCA6
A
1
1
210
1
MET
MODIFIED RESIDUE
MSE
112
1OUO
A
Q8DCA6
UNP
112
94
1
MET
MODIFIED RESIDUE
MSE
151
1OUO
A
Q8DCA6
UNP
151
133
1
MET
MODIFIED RESIDUE
MSE
161
1OUO
A
Q8DCA6
UNP
161
143
1
GLN
SEE REMARK 999
PRO
163
1OUO
A
Q8DCA6
UNP
163
145
1
THR
SEE REMARK 999
ASP
164
1OUO
A
Q8DCA6
UNP
164
146
1
GLU
SEE REMARK 999
ARG
165
1OUO
A
Q8DCA6
UNP
165
147
1
LEU
SEE REMARK 999
ALA
166
1OUO
A
Q8DCA6
UNP
166
148
1
MET
MODIFIED RESIDUE
MSE
177
1OUO
A
Q8DCA6
UNP
177
159
1
MET
MODIFIED RESIDUE
MSE
193
1OUO
A
Q8DCA6
UNP
193
175
2
2
4
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
ILE
48
A
ILE
30
A
GLN
51
A
GLN
33
A
LYS
54
A
LYS
36
A
PRO
57
A
PRO
39
A
ILE
76
A
ILE
58
A
HIS
80
A
HIS
62
A
LEU
119
A
LEU
101
A
ILE
123
A
ILE
105
A
ASN
134
A
ASN
116
A
PHE
135
A
PHE
117
A
LYS
159
A
LYS
141
A
MSE
161
A
MSE
143
A
CYS
149
A
CYS
131
A
ASN
154
A
ASN
136
A
VAL
144
A
VAL
126
A
TYR
146
A
TYR
128
BINDING SITE FOR RESIDUE MG A 494
Software
6
A
GLU
79
A
GLU
61
6
1_555
A
ASN
127
A
ASN
109
6
1_555
A
HOH
323
C
HOH
6
1_555
A
HOH
336
C
HOH
6
1_555
A
HOH
492
C
HOH
6
1_555
A
HOH
493
C
HOH
6
1_555
4
P 1 21 1