0.008326
0.004807
0.000000
0.000000
0.009614
0.000000
0.000000
0.000000
0.019037
0.00000
0.00000
0.00000
Xu, K.
Dedic, E.
Brodersen, D.E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
18
90.00
90.00
120.00
120.100
120.100
52.530
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
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
US
Proteins
PSFGEY
0867
1097-0134
84
892
899
10.1002/prot.25002
26833558
Structural analysis of the active site architecture of the VapC toxin from Shigella flexneri.
2016
100
1
CCD
2013-12-12
MARMOSAIC 225 mm CCD
SINGLE WAVELENGTH
M
x-ray
1
0.9795
1.0
I911-3
MAX II
0.9795
SYNCHROTRON
MAX II BEAMLINE I911-3
15620.947
tRNA(fMet)-specific endonuclease VapC
3.1.-.-
D7A
2
man
polymer
18.015
water
98
nat
water
RNase VapC,Toxin VapC
no
no
MHHHHHHLKFMLATNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDA
AAATHTGQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS
MHHHHHHLKFMLATNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDA
AAATHTGQIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS
A,B
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
sample
1
138
vapC, mvpA, stborf2, CP0245
623
Shigella flexneri
469008
Escherichia coli BL21(DE3)
Biological sequence
1
2.33
47.15
VAPOR DIFFUSION, SITTING DROP
7.0
0.2 M sodium malonate, 20% PEG 3350
292.15
diffrn_source
repository
Initial release
Database references
Data collection
1
0
2016-02-17
1
1
2016-06-15
1
2
2018-01-17
_diffrn_source.pdbx_synchrotron_site
China
Chinese Scholarship Council
5ECD contains the same protein with a different mutation
N
RCSB
Y
PDBE
2015-10-20
REL
REL
HOH
water
HOH
73
2
HOH
HOH
201
A
HOH
70
2
HOH
HOH
202
A
HOH
134
2
HOH
HOH
203
A
HOH
74
2
HOH
HOH
204
A
HOH
36
2
HOH
HOH
205
A
HOH
131
2
HOH
HOH
206
A
HOH
66
2
HOH
HOH
207
A
HOH
2
2
HOH
HOH
208
A
HOH
81
2
HOH
HOH
209
A
HOH
3
2
HOH
HOH
210
A
HOH
1
2
HOH
HOH
211
A
HOH
5
2
HOH
HOH
212
A
HOH
114
2
HOH
HOH
213
A
HOH
29
2
HOH
HOH
214
A
HOH
40
2
HOH
HOH
215
A
HOH
69
2
HOH
HOH
216
A
HOH
10
2
HOH
HOH
217
A
HOH
95
2
HOH
HOH
218
A
HOH
110
2
HOH
HOH
219
A
HOH
44
2
HOH
HOH
220
A
HOH
26
2
HOH
HOH
221
A
HOH
15
2
HOH
HOH
222
A
HOH
12
2
HOH
HOH
223
A
HOH
27
2
HOH
HOH
224
A
HOH
117
2
HOH
HOH
225
A
HOH
124
2
HOH
HOH
226
A
HOH
8
2
HOH
HOH
227
A
HOH
122
2
HOH
HOH
228
A
HOH
21
2
HOH
HOH
229
A
HOH
86
2
HOH
HOH
230
A
HOH
87
2
HOH
HOH
231
A
HOH
79
2
HOH
HOH
232
A
HOH
41
2
HOH
HOH
233
A
HOH
17
2
HOH
HOH
234
A
HOH
46
2
HOH
HOH
235
A
HOH
64
2
HOH
HOH
236
A
HOH
48
2
HOH
HOH
237
A
HOH
85
2
HOH
HOH
238
A
HOH
6
2
HOH
HOH
239
A
HOH
72
2
HOH
HOH
240
A
HOH
39
2
HOH
HOH
241
A
HOH
28
2
HOH
HOH
242
A
HOH
4
2
HOH
HOH
243
A
HOH
129
2
HOH
HOH
244
A
HOH
23
2
HOH
HOH
245
A
HOH
84
2
HOH
HOH
246
A
HOH
42
2
HOH
HOH
247
A
HOH
127
2
HOH
HOH
248
A
HOH
130
2
HOH
HOH
249
A
HOH
24
2
HOH
HOH
250
A
HOH
80
2
HOH
HOH
251
A
HOH
9
2
HOH
HOH
252
A
HOH
22
2
HOH
HOH
253
A
HOH
123
2
HOH
HOH
254
A
HOH
62
2
HOH
HOH
255
A
HOH
126
2
HOH
HOH
256
A
HOH
88
2
HOH
HOH
257
A
HOH
68
2
HOH
HOH
258
A
HOH
33
2
HOH
HOH
259
A
HOH
55
2
HOH
HOH
260
A
HOH
37
2
HOH
HOH
261
A
HOH
38
2
HOH
HOH
262
A
HOH
75
2
HOH
HOH
263
A
HOH
35
2
HOH
HOH
264
A
HOH
71
2
HOH
HOH
265
A
HOH
113
2
HOH
HOH
266
A
HOH
94
2
HOH
HOH
267
A
HOH
7
2
HOH
HOH
268
A
HOH
67
2
HOH
HOH
269
A
HOH
90
2
HOH
HOH
270
A
HOH
50
2
HOH
HOH
271
A
HOH
128
2
HOH
HOH
272
A
HOH
120
2
HOH
HOH
273
A
HOH
107
2
HOH
HOH
274
A
HOH
57
2
HOH
HOH
275
A
HOH
13
2
HOH
HOH
276
A
HOH
11
2
HOH
HOH
201
B
HOH
78
2
HOH
HOH
202
B
HOH
133
2
HOH
HOH
203
B
HOH
14
2
HOH
HOH
204
B
HOH
61
2
HOH
HOH
205
B
HOH
34
2
HOH
HOH
206
B
HOH
83
2
HOH
HOH
207
B
HOH
63
2
HOH
HOH
208
B
HOH
65
2
HOH
HOH
209
B
HOH
60
2
HOH
HOH
210
B
HOH
31
2
HOH
HOH
211
B
HOH
20
2
HOH
HOH
212
B
HOH
100
2
HOH
HOH
213
B
HOH
109
2
HOH
HOH
214
B
HOH
54
2
HOH
HOH
215
B
HOH
25
2
HOH
HOH
216
B
HOH
108
2
HOH
HOH
217
B
HOH
56
2
HOH
HOH
218
B
HOH
82
2
HOH
HOH
219
B
HOH
58
2
HOH
HOH
220
B
HOH
32
2
HOH
HOH
221
B
HOH
59
2
HOH
HOH
222
B
n
1
-5
A
n
2
-4
A
n
3
-3
A
n
4
-2
A
n
5
-1
A
n
6
0
A
HIS
1
n
7
HIS
1
A
LEU
2
n
8
LEU
2
A
LYS
3
n
9
LYS
3
A
PHE
4
n
10
PHE
4
A
MET
5
n
11
MET
5
A
LEU
6
n
12
LEU
6
A
ALA
7
n
13
ALA
7
A
THR
8
n
14
THR
8
A
ASN
9
n
15
ASN
9
A
ILE
10
n
16
ILE
10
A
CYS
11
n
17
CYS
11
A
ILE
12
n
18
ILE
12
A
PHE
13
n
19
PHE
13
A
THR
14
n
20
THR
14
A
ILE
15
n
21
ILE
15
A
LYS
16
n
22
LYS
16
A
ASN
17
n
23
ASN
17
A
LYS
18
n
24
LYS
18
A
PRO
19
n
25
PRO
19
A
ALA
20
n
26
ALA
20
A
SER
21
n
27
SER
21
A
VAL
22
n
28
VAL
22
A
ARG
23
n
29
ARG
23
A
GLU
24
n
30
GLU
24
A
ARG
25
n
31
ARG
25
A
PHE
26
n
32
PHE
26
A
ASN
27
n
33
ASN
27
A
LEU
28
n
34
LEU
28
A
ASN
29
n
35
ASN
29
A
GLN
30
n
36
GLN
30
A
GLY
31
n
37
GLY
31
A
LYS
32
n
38
LYS
32
A
MET
33
n
39
MET
33
A
CYS
34
n
40
CYS
34
A
ILE
35
n
41
ILE
35
A
SER
36
n
42
SER
36
A
SER
37
n
43
SER
37
A
VAL
38
n
44
VAL
38
A
THR
39
n
45
THR
39
A
LEU
40
n
46
LEU
40
A
MET
41
n
47
MET
41
A
GLU
42
n
48
GLU
42
A
LEU
43
n
49
LEU
43
A
ILE
44
n
50
ILE
44
A
TYR
45
n
51
TYR
45
A
GLY
46
n
52
GLY
46
A
ALA
47
n
53
ALA
47
A
GLU
48
n
54
GLU
48
A
LYS
49
n
55
LYS
49
A
SER
50
n
56
SER
50
A
GLN
51
n
57
GLN
51
A
MET
52
n
58
MET
52
A
PRO
53
n
59
PRO
53
A
GLU
54
n
60
GLU
54
A
ARG
55
n
61
ARG
55
A
ASN
56
n
62
ASN
56
A
LEU
57
n
63
LEU
57
A
ALA
58
n
64
ALA
58
A
VAL
59
n
65
VAL
59
A
ILE
60
n
66
ILE
60
A
GLU
61
n
67
GLU
61
A
GLY
62
n
68
GLY
62
A
PHE
63
n
69
PHE
63
A
VAL
64
n
70
VAL
64
A
SER
65
n
71
SER
65
A
ARG
66
n
72
ARG
66
A
ILE
67
n
73
ILE
67
A
ASP
68
n
74
ASP
68
A
VAL
69
n
75
VAL
69
A
LEU
70
n
76
LEU
70
A
ASP
71
n
77
ASP
71
A
TYR
72
n
78
TYR
72
A
ASP
73
n
79
ASP
73
A
ALA
74
n
80
ALA
74
A
ALA
75
n
81
ALA
75
A
ALA
76
n
82
ALA
76
A
ALA
77
n
83
ALA
77
A
THR
78
n
84
THR
78
A
HIS
79
n
85
HIS
79
A
THR
80
n
86
THR
80
A
GLY
81
n
87
GLY
81
A
GLN
82
n
88
GLN
82
A
ILE
83
n
89
ILE
83
A
ARG
84
n
90
ARG
84
A
ALA
85
n
91
ALA
85
A
GLU
86
n
92
GLU
86
A
LEU
87
n
93
LEU
87
A
ALA
88
n
94
ALA
88
A
ARG
89
n
95
ARG
89
A
GLN
90
n
96
GLN
90
A
GLY
91
n
97
GLY
91
A
ARG
92
n
98
ARG
92
A
PRO
93
n
99
PRO
93
A
VAL
94
n
100
VAL
94
A
GLY
95
n
101
GLY
95
A
PRO
96
n
102
PRO
96
A
PHE
97
n
103
PHE
97
A
ASP
98
n
104
ASP
98
A
GLN
99
n
105
GLN
99
A
MET
100
n
106
MET
100
A
ILE
101
n
107
ILE
101
A
ALA
102
n
108
ALA
102
A
GLY
103
n
109
GLY
103
A
HIS
104
n
110
HIS
104
A
ALA
105
n
111
ALA
105
A
ARG
106
n
112
ARG
106
A
SER
107
n
113
SER
107
A
ARG
108
n
114
ARG
108
A
GLY
109
n
115
GLY
109
A
LEU
110
n
116
LEU
110
A
ILE
111
n
117
ILE
111
A
ILE
112
n
118
ILE
112
A
VAL
113
n
119
VAL
113
A
THR
114
n
120
THR
114
A
ASN
115
n
121
ASN
115
A
ASN
116
n
122
ASN
116
A
THR
117
n
123
THR
117
A
ARG
118
n
124
ARG
118
A
GLU
119
n
125
GLU
119
A
PHE
120
n
126
PHE
120
A
GLU
121
n
127
GLU
121
A
ARG
122
n
128
ARG
122
A
VAL
123
n
129
VAL
123
A
GLY
124
n
130
GLY
124
A
GLY
125
n
131
GLY
125
A
LEU
126
n
132
LEU
126
A
ARG
127
n
133
ARG
127
A
THR
128
n
134
THR
128
A
GLU
129
n
135
GLU
129
A
ASP
130
n
136
ASP
130
A
TRP
131
n
137
TRP
131
A
SER
132
n
138
SER
132
A
n
1
-5
B
n
2
-4
B
n
3
-3
B
n
4
-2
B
n
5
-1
B
n
6
0
B
HIS
1
n
7
HIS
1
B
LEU
2
n
8
LEU
2
B
LYS
3
n
9
LYS
3
B
PHE
4
n
10
PHE
4
B
MET
5
n
11
MET
5
B
LEU
6
n
12
LEU
6
B
ALA
7
n
13
ALA
7
B
THR
8
n
14
THR
8
B
ASN
9
n
15
ASN
9
B
ILE
10
n
16
ILE
10
B
CYS
11
n
17
CYS
11
B
ILE
12
n
18
ILE
12
B
PHE
13
n
19
PHE
13
B
THR
14
n
20
THR
14
B
ILE
15
n
21
ILE
15
B
LYS
16
n
22
LYS
16
B
ASN
17
n
23
ASN
17
B
LYS
18
n
24
LYS
18
B
n
25
19
B
n
26
20
B
n
27
21
B
n
28
22
B
n
29
23
B
n
30
24
B
n
31
25
B
n
32
26
B
n
33
27
B
LEU
28
n
34
LEU
28
B
ASN
29
n
35
ASN
29
B
GLN
30
n
36
GLN
30
B
GLY
31
n
37
GLY
31
B
LYS
32
n
38
LYS
32
B
MET
33
n
39
MET
33
B
CYS
34
n
40
CYS
34
B
ILE
35
n
41
ILE
35
B
SER
36
n
42
SER
36
B
SER
37
n
43
SER
37
B
VAL
38
n
44
VAL
38
B
THR
39
n
45
THR
39
B
LEU
40
n
46
LEU
40
B
MET
41
n
47
MET
41
B
GLU
42
n
48
GLU
42
B
LEU
43
n
49
LEU
43
B
ILE
44
n
50
ILE
44
B
TYR
45
n
51
TYR
45
B
GLY
46
n
52
GLY
46
B
ALA
47
n
53
ALA
47
B
GLU
48
n
54
GLU
48
B
LYS
49
n
55
LYS
49
B
SER
50
n
56
SER
50
B
GLN
51
n
57
GLN
51
B
MET
52
n
58
MET
52
B
PRO
53
n
59
PRO
53
B
GLU
54
n
60
GLU
54
B
ARG
55
n
61
ARG
55
B
ASN
56
n
62
ASN
56
B
LEU
57
n
63
LEU
57
B
ALA
58
n
64
ALA
58
B
VAL
59
n
65
VAL
59
B
ILE
60
n
66
ILE
60
B
GLU
61
n
67
GLU
61
B
GLY
62
n
68
GLY
62
B
PHE
63
n
69
PHE
63
B
VAL
64
n
70
VAL
64
B
SER
65
n
71
SER
65
B
ARG
66
n
72
ARG
66
B
ILE
67
n
73
ILE
67
B
ASP
68
n
74
ASP
68
B
VAL
69
n
75
VAL
69
B
LEU
70
n
76
LEU
70
B
ASP
71
n
77
ASP
71
B
TYR
72
n
78
TYR
72
B
ASP
73
n
79
ASP
73
B
ALA
74
n
80
ALA
74
B
ALA
75
n
81
ALA
75
B
ALA
76
n
82
ALA
76
B
ALA
77
n
83
ALA
77
B
THR
78
n
84
THR
78
B
HIS
79
n
85
HIS
79
B
THR
80
n
86
THR
80
B
GLY
81
n
87
GLY
81
B
GLN
82
n
88
GLN
82
B
ILE
83
n
89
ILE
83
B
ARG
84
n
90
ARG
84
B
ALA
85
n
91
ALA
85
B
GLU
86
n
92
GLU
86
B
LEU
87
n
93
LEU
87
B
ALA
88
n
94
ALA
88
B
ARG
89
n
95
ARG
89
B
GLN
90
n
96
GLN
90
B
GLY
91
n
97
GLY
91
B
ARG
92
n
98
ARG
92
B
PRO
93
n
99
PRO
93
B
VAL
94
n
100
VAL
94
B
GLY
95
n
101
GLY
95
B
PRO
96
n
102
PRO
96
B
PHE
97
n
103
PHE
97
B
ASP
98
n
104
ASP
98
B
GLN
99
n
105
GLN
99
B
MET
100
n
106
MET
100
B
ILE
101
n
107
ILE
101
B
ALA
102
n
108
ALA
102
B
GLY
103
n
109
GLY
103
B
HIS
104
n
110
HIS
104
B
ALA
105
n
111
ALA
105
B
ARG
106
n
112
ARG
106
B
SER
107
n
113
SER
107
B
ARG
108
n
114
ARG
108
B
GLY
109
n
115
GLY
109
B
LEU
110
n
116
LEU
110
B
ILE
111
n
117
ILE
111
B
ILE
112
n
118
ILE
112
B
VAL
113
n
119
VAL
113
B
THR
114
n
120
THR
114
B
ASN
115
n
121
ASN
115
B
ASN
116
n
122
ASN
116
B
THR
117
n
123
THR
117
B
ARG
118
n
124
ARG
118
B
GLU
119
n
125
GLU
119
B
PHE
120
n
126
PHE
120
B
GLU
121
n
127
GLU
121
B
ARG
122
n
128
ARG
122
B
VAL
123
n
129
VAL
123
B
GLY
124
n
130
GLY
124
B
GLY
125
n
131
GLY
125
B
LEU
126
n
132
LEU
126
B
ARG
127
n
133
ARG
127
B
THR
128
n
134
THR
128
B
GLU
129
n
135
GLU
129
B
ASP
130
n
136
ASP
130
B
TRP
131
n
137
TRP
131
B
SER
132
n
138
SER
132
B
7.2223
0.3473
-2.3881
1.6086
-0.0421
2.8054
-0.6098
-0.3808
-0.3815
0.1388
0.2567
0.0487
0.3384
0.2283
0.2280
0.3183
0.0841
-0.0215
0.2823
-0.0277
0.2039
refined
-23.8041
-7.3765
13.5334
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
all
author_and_software_defined_assembly
PISA
2
dimeric
2210
-21
11650
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
LEU
70
A
O
LEU
76
A
N
ILE
35
A
N
ILE
41
A
O
CYS
34
A
O
CYS
40
A
N
LEU
6
A
N
LEU
12
A
N
MET
5
A
N
MET
11
A
O
ILE
111
A
O
ILE
117
A
N
ILE
112
A
N
ILE
118
A
O
GLU
129
A
O
GLU
135
B
O
LEU
70
B
O
LEU
76
B
N
ILE
35
B
N
ILE
41
B
O
CYS
34
B
O
CYS
40
B
N
LEU
6
B
N
LEU
12
B
N
MET
5
B
N
MET
11
B
O
ILE
111
B
O
ILE
117
B
N
ILE
112
B
N
ILE
118
B
O
GLU
129
B
O
GLU
135
1
A
CG
HIS
1
A
CG
HIS
7
1
Y
1
A
ND1
HIS
1
A
ND1
HIS
7
1
Y
1
A
CD2
HIS
1
A
CD2
HIS
7
1
Y
1
A
CE1
HIS
1
A
CE1
HIS
7
1
Y
1
A
NE2
HIS
1
A
NE2
HIS
7
1
Y
1
A
CD
LYS
3
A
CD
LYS
9
1
Y
1
A
CE
LYS
3
A
CE
LYS
9
1
Y
1
A
NZ
LYS
3
A
NZ
LYS
9
1
Y
1
A
CE
LYS
18
A
CE
LYS
24
1
Y
1
A
NZ
LYS
18
A
NZ
LYS
24
1
Y
1
A
CD1
LEU
28
A
CD1
LEU
34
1
Y
1
A
CD2
LEU
28
A
CD2
LEU
34
1
Y
1
A
CD
GLN
30
A
CD
GLN
36
1
Y
1
A
OE1
GLN
30
A
OE1
GLN
36
1
Y
1
A
NE2
GLN
30
A
NE2
GLN
36
1
Y
1
A
CZ
ARG
89
A
CZ
ARG
95
1
Y
1
A
NH1
ARG
89
A
NH1
ARG
95
1
Y
1
A
NH2
ARG
89
A
NH2
ARG
95
1
Y
1
B
CG
HIS
1
B
CG
HIS
7
1
Y
1
B
ND1
HIS
1
B
ND1
HIS
7
1
Y
1
B
CD2
HIS
1
B
CD2
HIS
7
1
Y
1
B
CE1
HIS
1
B
CE1
HIS
7
1
Y
1
B
NE2
HIS
1
B
NE2
HIS
7
1
Y
1
B
CD1
LEU
6
B
CD1
LEU
12
1
Y
1
B
CD2
LEU
6
B
CD2
LEU
12
1
Y
1
B
CG
ASN
17
B
CG
ASN
23
1
Y
1
B
OD1
ASN
17
B
OD1
ASN
23
1
Y
1
B
ND2
ASN
17
B
ND2
ASN
23
1
Y
1
B
CG
LYS
18
B
CG
LYS
24
1
Y
1
B
CD
LYS
18
B
CD
LYS
24
1
Y
1
B
CE
LYS
18
B
CE
LYS
24
1
Y
1
B
NZ
LYS
18
B
NZ
LYS
24
1
Y
1
B
CG
LEU
28
B
CG
LEU
34
1
Y
1
B
CD1
LEU
28
B
CD1
LEU
34
1
Y
1
B
CD2
LEU
28
B
CD2
LEU
34
1
Y
1
B
CG
GLN
30
B
CG
GLN
36
1
Y
1
B
CD
GLN
30
B
CD
GLN
36
1
Y
1
B
OE1
GLN
30
B
OE1
GLN
36
1
Y
1
B
NE2
GLN
30
B
NE2
GLN
36
1
Y
1
B
CG
LYS
32
B
CG
LYS
38
1
Y
1
B
CD
LYS
32
B
CD
LYS
38
1
Y
1
B
CE
LYS
32
B
CE
LYS
38
1
Y
1
B
NZ
LYS
32
B
NZ
LYS
38
1
Y
1
B
CG
ARG
55
B
CG
ARG
61
1
Y
1
B
CD
ARG
55
B
CD
ARG
61
1
Y
1
B
NE
ARG
55
B
NE
ARG
61
1
Y
1
B
CZ
ARG
55
B
CZ
ARG
61
1
Y
1
B
NH1
ARG
55
B
NH1
ARG
61
1
Y
1
B
NH2
ARG
55
B
NH2
ARG
61
1
Y
1
B
CG
GLU
86
B
CG
GLU
92
1
Y
1
B
CD
GLU
86
B
CD
GLU
92
1
Y
1
B
OE1
GLU
86
B
OE1
GLU
92
1
Y
1
B
OE2
GLU
86
B
OE2
GLU
92
1
Y
1
B
CD
ARG
92
B
CD
ARG
98
1
Y
1
B
NE
ARG
92
B
NE
ARG
98
1
Y
1
B
CZ
ARG
92
B
CZ
ARG
98
1
Y
1
B
NH1
ARG
92
B
NH1
ARG
98
1
Y
1
B
NH2
ARG
92
B
NH2
ARG
98
1
Y
1
B
CG
ASN
115
B
CG
ASN
121
1
Y
1
B
OD1
ASN
115
B
OD1
ASN
121
1
Y
1
B
ND2
ASN
115
B
ND2
ASN
121
1
Y
1
B
CG
ARG
118
B
CG
ARG
124
1
Y
1
B
CD
ARG
118
B
CD
ARG
124
1
Y
1
B
NE
ARG
118
B
NE
ARG
124
1
Y
1
B
CZ
ARG
118
B
CZ
ARG
124
1
Y
1
B
NH1
ARG
118
B
NH1
ARG
124
1
Y
1
B
NH2
ARG
118
B
NH2
ARG
124
1
Y
1
B
CG
GLU
121
B
CG
GLU
127
1
Y
1
B
CD
GLU
121
B
CD
GLU
127
1
Y
1
B
OE1
GLU
121
B
OE1
GLU
127
1
Y
1
B
OE2
GLU
121
B
OE2
GLU
127
1
Y
1
B
CZ
ARG
122
B
CZ
ARG
128
1
Y
1
B
NH1
ARG
122
B
NH1
ARG
128
1
Y
1
B
NH2
ARG
122
B
NH2
ARG
128
1
Y
1
B
CG1
VAL
123
B
CG1
VAL
129
1
Y
1
B
CG2
VAL
123
B
CG2
VAL
129
1
Y
1
A
MET
-5
A
MET
1
1
Y
1
A
HIS
-4
A
HIS
2
1
Y
1
A
HIS
-3
A
HIS
3
1
Y
1
A
HIS
-2
A
HIS
4
1
Y
1
A
HIS
-1
A
HIS
5
1
Y
1
A
HIS
0
A
HIS
6
1
Y
1
B
MET
-5
B
MET
1
1
Y
1
B
HIS
-4
B
HIS
2
1
Y
1
B
HIS
-3
B
HIS
3
1
Y
1
B
HIS
-2
B
HIS
4
1
Y
1
B
HIS
-1
B
HIS
5
1
Y
1
B
HIS
0
B
HIS
6
1
Y
1
B
PRO
19
B
PRO
25
1
Y
1
B
ALA
20
B
ALA
26
1
Y
1
B
SER
21
B
SER
27
1
Y
1
B
VAL
22
B
VAL
28
1
Y
1
B
ARG
23
B
ARG
29
1
Y
1
B
GLU
24
B
GLU
30
1
Y
1
B
ARG
25
B
ARG
31
1
Y
1
B
PHE
26
B
PHE
32
1
Y
1
B
ASN
27
B
ASN
33
1
Y
1
A
ASN
116
-105.29
-82.90
1
A
THR
117
73.90
-22.87
1
B
ASN
17
55.17
-119.54
1
B
GLN
30
58.81
139.58
0.2259
0.1888
0.1925
1.940
23.44
1925
19319
9.96
92.44
0.29
1
FREE R-VALUE
1.92
MOLECULAR REPLACEMENT
26.21
0.90
1.11
ML
FLAT BULK SOLVENT MODEL
1.940
23.44
98
2017
0
0
1919
0.008
1955
1.002
2640
13.306
711
0.046
305
0.005
344
0.6155
0.5954
1.9885
120
1071
79.00
0.2676
0.2356
2.0423
146
1337
100.00
0.2803
0.2196
2.1023
155
1369
100.00
0.2753
0.2021
2.1702
141
1310
100.00
0.2587
0.2168
2.2477
91
806
97.00
0.2705
0.2282
2.3376
91
821
96.00
0.2441
0.2029
2.4439
147
1342
100.00
0.2456
0.2055
2.5727
149
1352
100.00
0.2686
0.1988
2.7337
150
1343
100.00
0.2644
0.2066
2.9444
149
1330
100.00
0.2501
0.2033
3.2402
149
1347
100.00
0.2199
0.1789
3.7078
151
1353
100.00
0.1652
0.1453
4.6666
147
1337
100.00
0.1747
0.1622
25.2874
139
1276
94.00
1.94
23.44
5ECW
1751
1
30.77
6.25
92.4
refinement
PHENIX
dev_1839
data reduction
XDS
data scaling
XSCALE
phasing
PHENIX
tRNA(fMet)-specific endonuclease VapC (E.C.3.1.-.-)
Structure of the Shigella flexneri VapC mutant D7A
1
N
N
1
N
N
2
N
N
2
N
N
A
ALA
7
A
ALA
13
HELX_P
A
ASN
17
A
ASN
23
1
AA1
11
A
PRO
19
A
PRO
25
HELX_P
A
ASN
29
A
ASN
35
1
AA2
11
A
SER
37
A
SER
43
HELX_P
A
SER
50
A
SER
56
1
AA3
14
A
MET
52
A
MET
58
HELX_P
A
SER
65
A
SER
71
1
AA4
14
A
ASP
73
A
ASP
79
HELX_P
A
GLY
91
A
GLY
97
1
AA5
19
A
GLY
95
A
GLY
101
HELX_P
A
ARG
108
A
ARG
114
1
AA6
14
B
ALA
7
B
ALA
13
HELX_P
B
ASN
17
B
ASN
23
1
AA7
11
B
SER
37
B
SER
43
HELX_P
B
LYS
49
B
LYS
55
1
AA8
13
B
MET
52
B
MET
58
HELX_P
B
SER
65
B
SER
71
1
AA9
14
B
ASP
73
B
ASP
79
HELX_P
B
GLY
91
B
GLY
97
1
AB1
19
B
GLY
95
B
GLY
101
HELX_P
B
ARG
108
B
ARG
114
1
AB2
14
B
GLU
119
B
GLU
125
HELX_P
B
VAL
123
B
VAL
129
5
AB3
5
HYDROLASE
Toxin, PIN-domain, hydrolase
A
LYS
18
A
LYS
24
1
A
PRO
19
A
PRO
25
-7.72
VAPC_SHIFL
UNP
1
2
O06662
LKFMLDTNICIFTIKNKPASVRERFNLNQGKMCISSVTLMELIYGAEKSQMPERNLAVIEGFVSRIDVLDYDAAAATHTG
QIRAELARQGRPVGPFDQMIAGHARSRGLIIVTNNTREFERVGGLRTEDWS
2
132
5ECW
2
132
O06662
A
1
8
138
2
132
5ECW
2
132
O06662
B
1
8
138
1
initiating methionine
MET
-5
5ECW
A
O06662
UNP
1
1
expression tag
HIS
-4
5ECW
A
O06662
UNP
2
1
expression tag
HIS
-3
5ECW
A
O06662
UNP
3
1
expression tag
HIS
-2
5ECW
A
O06662
UNP
4
1
expression tag
HIS
-1
5ECW
A
O06662
UNP
5
1
expression tag
HIS
0
5ECW
A
O06662
UNP
6
1
expression tag
HIS
1
5ECW
A
O06662
UNP
7
1
ASP
engineered mutation
ALA
7
5ECW
A
O06662
UNP
7
13
2
initiating methionine
MET
-5
5ECW
B
O06662
UNP
1
2
expression tag
HIS
-4
5ECW
B
O06662
UNP
2
2
expression tag
HIS
-3
5ECW
B
O06662
UNP
3
2
expression tag
HIS
-2
5ECW
B
O06662
UNP
4
2
expression tag
HIS
-1
5ECW
B
O06662
UNP
5
2
expression tag
HIS
0
5ECW
B
O06662
UNP
6
2
expression tag
HIS
1
5ECW
B
O06662
UNP
7
2
ASP
engineered mutation
ALA
7
5ECW
B
O06662
UNP
7
13
5
5
parallel
parallel
parallel
parallel
parallel
parallel
parallel
parallel
A
ASP
68
A
ASP
74
A
LEU
70
A
LEU
76
A
MET
33
A
MET
39
A
SER
36
A
SER
42
A
PHE
4
A
PHE
10
A
LEU
6
A
LEU
12
A
ILE
111
A
ILE
117
A
VAL
113
A
VAL
119
A
THR
128
A
THR
134
A
GLU
129
A
GLU
135
B
ASP
68
B
ASP
74
B
LEU
70
B
LEU
76
B
MET
33
B
MET
39
B
SER
36
B
SER
42
B
PHE
4
B
PHE
10
B
LEU
6
B
LEU
12
B
ILE
111
B
ILE
117
B
VAL
113
B
VAL
119
B
THR
128
B
THR
134
B
GLU
129
B
GLU
135
146
H 3