0.024881
0.000000
0.009146
0.000000
0.025931
0.000000
0.000000
0.000000
0.018759
0.00000
0.00000
0.00000
Miyatake, H.
Hasegawa, T.
Yamano, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.00
110.18
90.00
40.191
38.564
56.794
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
I -1
126.904
IODIDE ION
non-polymer
C9 H10 I N O3
307.085
n
3-IODO-TYROSINE
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 H9 I2 N O3
432.982
n
3,5-DIIODOTYROSINE
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
DK
ACTA CRYSTALLOGR.,SECT.D
ABCRE6
0766
0907-4449
62
280
289
10.1107/S0907444905041909
16510975
New methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL)
2006
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
Osmic Cu CMF
IMAGE PLATE
2005-08-03
RIGAKU RAXIS IV
Osmic Cu CMF
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU FR-E
21734.510
Endo-1,4-beta-xylanase 2
3.2.1.8
1
nat
polymer
126.904
IODIDE ION
1
syn
non-polymer
18.015
water
52
nat
water
Xylanase 2, 1,4- beta-D-xylan xylanohydrolase 2
no
yes
TIQPGTG(IYR)NNGYFYSYWNDGHGGVTYTNGPGGQFSVNWSNSGNFVGGKGWQPGTKNKVINFSGSYNPNGNS(IYR)
LSVYGWSRNPLIEYYIVENFGT(IYR)NPSTGATKLGEVTSDGSVYDIYRTQRVNQPSIIGTATF(TYI)QYWSVRRNHR
SSGSVNTANHFNAWAQQGLTLGTMD(TYI)QIVAVEG(IYR)FSSGSASITVS
TIQPGTGYNNGYFYSYWNDGHGGVTYTNGPGGQFSVNWSNSGNFVGGKGWQPGTKNKVINFSGSYNPNGNSYLSVYGWSR
NPLIEYYIVENFGTYNPSTGATKLGEVTSDGSVYDIYRTQRVNQPSIIGTATFYQYWSVRRNHRSSGSVNTANHFNAWAQ
QGLTLGTMDYQIVAVEGYFSSGSASITVS
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
Hypocrea
sample
51453
Hypocrea jecorina
1
1.90
35.27
VAPOR DIFFUSION, HANGING DROP
4.3
1.5M ammonium sulfate, 0.1M Na citrate , pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
repository
Initial release
Version format compliance
Version format compliance
1
0
2006-07-11
1
1
2008-04-30
1
2
2011-07-13
VIL-thaumatin
HYPER-VIL-thaumatin
HYPER-VIL-trypsine
HYPER-VIL-lysozyme
VIL-xylanase
PDBJ
Y
PDBJ
2005-12-09
REL
REL
IOD
IODIDE ION
HOH
water
IOD
200
2
IOD
IOD
200
A
HOH
1
3
HOH
HOH
201
A
HOH
2
3
HOH
HOH
202
A
HOH
3
3
HOH
HOH
203
A
HOH
4
3
HOH
HOH
204
A
HOH
5
3
HOH
HOH
205
A
HOH
6
3
HOH
HOH
206
A
HOH
7
3
HOH
HOH
207
A
HOH
8
3
HOH
HOH
208
A
HOH
9
3
HOH
HOH
209
A
HOH
10
3
HOH
HOH
210
A
HOH
11
3
HOH
HOH
211
A
HOH
12
3
HOH
HOH
212
A
HOH
13
3
HOH
HOH
213
A
HOH
14
3
HOH
HOH
214
A
HOH
15
3
HOH
HOH
215
A
HOH
16
3
HOH
HOH
216
A
HOH
17
3
HOH
HOH
217
A
HOH
18
3
HOH
HOH
218
A
HOH
19
3
HOH
HOH
219
A
HOH
20
3
HOH
HOH
220
A
HOH
21
3
HOH
HOH
221
A
HOH
22
3
HOH
HOH
222
A
HOH
23
3
HOH
HOH
223
A
HOH
24
3
HOH
HOH
224
A
HOH
25
3
HOH
HOH
225
A
HOH
26
3
HOH
HOH
226
A
HOH
27
3
HOH
HOH
227
A
HOH
28
3
HOH
HOH
228
A
HOH
29
3
HOH
HOH
229
A
HOH
30
3
HOH
HOH
230
A
HOH
31
3
HOH
HOH
231
A
HOH
32
3
HOH
HOH
232
A
HOH
33
3
HOH
HOH
233
A
HOH
34
3
HOH
HOH
234
A
HOH
35
3
HOH
HOH
235
A
HOH
36
3
HOH
HOH
236
A
HOH
37
3
HOH
HOH
237
A
HOH
38
3
HOH
HOH
238
A
HOH
39
3
HOH
HOH
239
A
HOH
40
3
HOH
HOH
240
A
HOH
41
3
HOH
HOH
241
A
HOH
42
3
HOH
HOH
242
A
HOH
43
3
HOH
HOH
243
A
HOH
44
3
HOH
HOH
244
A
HOH
45
3
HOH
HOH
245
A
HOH
46
3
HOH
HOH
246
A
HOH
47
3
HOH
HOH
247
A
HOH
48
3
HOH
HOH
248
A
HOH
49
3
HOH
HOH
249
A
HOH
50
3
HOH
HOH
250
A
HOH
51
3
HOH
HOH
251
A
HOH
52
3
HOH
HOH
252
A
THR
2
n
1
THR
2
A
ILE
3
n
2
ILE
3
A
GLN
4
n
3
GLN
4
A
PRO
5
n
4
PRO
5
A
GLY
6
n
5
GLY
6
A
THR
7
n
6
THR
7
A
GLY
8
n
7
GLY
8
A
IYR
9
n
8
IYR
9
A
ASN
10
n
9
ASN
10
A
ASN
11
n
10
ASN
11
A
GLY
12
n
11
GLY
12
A
TYR
13
n
12
TYR
13
A
PHE
14
n
13
PHE
14
A
TYR
15
n
14
TYR
15
A
SER
16
n
15
SER
16
A
TYR
17
n
16
TYR
17
A
TRP
18
n
17
TRP
18
A
ASN
19
n
18
ASN
19
A
ASP
20
n
19
ASP
20
A
GLY
21
n
20
GLY
21
A
HIS
22
n
21
HIS
22
A
GLY
23
n
22
GLY
23
A
GLY
24
n
23
GLY
24
A
VAL
25
n
24
VAL
25
A
THR
26
n
25
THR
26
A
TYR
27
n
26
TYR
27
A
THR
28
n
27
THR
28
A
ASN
29
n
28
ASN
29
A
GLY
30
n
29
GLY
30
A
PRO
31
n
30
PRO
31
A
GLY
32
n
31
GLY
32
A
GLY
33
n
32
GLY
33
A
GLN
34
n
33
GLN
34
A
PHE
35
n
34
PHE
35
A
SER
36
n
35
SER
36
A
VAL
37
n
36
VAL
37
A
ASN
38
n
37
ASN
38
A
TRP
39
n
38
TRP
39
A
SER
40
n
39
SER
40
A
ASN
41
n
40
ASN
41
A
SER
42
n
41
SER
42
A
GLY
43
n
42
GLY
43
A
ASN
44
n
43
ASN
44
A
PHE
45
n
44
PHE
45
A
VAL
46
n
45
VAL
46
A
GLY
47
n
46
GLY
47
A
GLY
48
n
47
GLY
48
A
LYS
49
n
48
LYS
49
A
GLY
50
n
49
GLY
50
A
TRP
51
n
50
TRP
51
A
GLN
52
n
51
GLN
52
A
PRO
53
n
52
PRO
53
A
GLY
54
n
53
GLY
54
A
THR
55
n
54
THR
55
A
LYS
56
n
55
LYS
56
A
ASN
57
n
56
ASN
57
A
LYS
58
n
57
LYS
58
A
VAL
59
n
58
VAL
59
A
ILE
60
n
59
ILE
60
A
ASN
61
n
60
ASN
61
A
PHE
62
n
61
PHE
62
A
SER
63
n
62
SER
63
A
GLY
64
n
63
GLY
64
A
SER
65
n
64
SER
65
A
TYR
66
n
65
TYR
66
A
ASN
67
n
66
ASN
67
A
PRO
68
n
67
PRO
68
A
ASN
69
n
68
ASN
69
A
GLY
70
n
69
GLY
70
A
ASN
71
n
70
ASN
71
A
SER
72
n
71
SER
72
A
IYR
73
n
72
IYR
73
A
LEU
74
n
73
LEU
74
A
SER
75
n
74
SER
75
A
VAL
76
n
75
VAL
76
A
TYR
77
n
76
TYR
77
A
GLY
78
n
77
GLY
78
A
TRP
79
n
78
TRP
79
A
SER
80
n
79
SER
80
A
ARG
81
n
80
ARG
81
A
ASN
82
n
81
ASN
82
A
PRO
83
n
82
PRO
83
A
LEU
84
n
83
LEU
84
A
ILE
85
n
84
ILE
85
A
GLU
86
n
85
GLU
86
A
TYR
87
n
86
TYR
87
A
TYR
88
n
87
TYR
88
A
ILE
89
n
88
ILE
89
A
VAL
90
n
89
VAL
90
A
GLU
91
n
90
GLU
91
A
ASN
92
n
91
ASN
92
A
PHE
93
n
92
PHE
93
A
GLY
94
n
93
GLY
94
A
THR
95
n
94
THR
95
A
IYR
96
n
95
IYR
96
A
ASN
97
n
96
ASN
97
A
PRO
98
n
97
PRO
98
A
SER
99
n
98
SER
99
A
THR
100
n
99
THR
100
A
GLY
101
n
100
GLY
101
A
ALA
102
n
101
ALA
102
A
THR
103
n
102
THR
103
A
LYS
104
n
103
LYS
104
A
LEU
105
n
104
LEU
105
A
GLY
106
n
105
GLY
106
A
GLU
107
n
106
GLU
107
A
VAL
108
n
107
VAL
108
A
THR
109
n
108
THR
109
A
SER
110
n
109
SER
110
A
ASP
111
n
110
ASP
111
A
GLY
112
n
111
GLY
112
A
SER
113
n
112
SER
113
A
VAL
114
n
113
VAL
114
A
TYR
115
n
114
TYR
115
A
ASP
116
n
115
ASP
116
A
ILE
117
n
116
ILE
117
A
TYR
118
n
117
TYR
118
A
ARG
119
n
118
ARG
119
A
THR
120
n
119
THR
120
A
GLN
121
n
120
GLN
121
A
ARG
122
n
121
ARG
122
A
VAL
123
n
122
VAL
123
A
ASN
124
n
123
ASN
124
A
GLN
125
n
124
GLN
125
A
PRO
126
n
125
PRO
126
A
SER
127
n
126
SER
127
A
ILE
128
n
127
ILE
128
A
ILE
129
n
128
ILE
129
A
GLY
130
n
129
GLY
130
A
THR
131
n
130
THR
131
A
ALA
132
n
131
ALA
132
A
THR
133
n
132
THR
133
A
PHE
134
n
133
PHE
134
A
TYI
135
n
134
TYI
135
A
GLN
136
n
135
GLN
136
A
TYR
137
n
136
TYR
137
A
TRP
138
n
137
TRP
138
A
SER
139
n
138
SER
139
A
VAL
140
n
139
VAL
140
A
ARG
141
n
140
ARG
141
A
ARG
142
n
141
ARG
142
A
ASN
143
n
142
ASN
143
A
HIS
144
n
143
HIS
144
A
ARG
145
n
144
ARG
145
A
SER
146
n
145
SER
146
A
SER
147
n
146
SER
147
A
GLY
148
n
147
GLY
148
A
SER
149
n
148
SER
149
A
VAL
150
n
149
VAL
150
A
ASN
151
n
150
ASN
151
A
THR
152
n
151
THR
152
A
ALA
153
n
152
ALA
153
A
ASN
154
n
153
ASN
154
A
HIS
155
n
154
HIS
155
A
PHE
156
n
155
PHE
156
A
ASN
157
n
156
ASN
157
A
ALA
158
n
157
ALA
158
A
TRP
159
n
158
TRP
159
A
ALA
160
n
159
ALA
160
A
GLN
161
n
160
GLN
161
A
GLN
162
n
161
GLN
162
A
GLY
163
n
162
GLY
163
A
LEU
164
n
163
LEU
164
A
THR
165
n
164
THR
165
A
LEU
166
n
165
LEU
166
A
GLY
167
n
166
GLY
167
A
THR
168
n
167
THR
168
A
MET
169
n
168
MET
169
A
ASP
170
n
169
ASP
170
A
TYI
171
n
170
TYI
171
A
GLN
172
n
171
GLN
172
A
ILE
173
n
172
ILE
173
A
VAL
174
n
173
VAL
174
A
ALA
175
n
174
ALA
175
A
VAL
176
n
175
VAL
176
A
GLU
177
n
176
GLU
177
A
GLY
178
n
177
GLY
178
A
IYR
179
n
178
IYR
179
A
PHE
180
n
179
PHE
180
A
SER
181
n
180
SER
181
A
SER
182
n
181
SER
182
A
GLY
183
n
182
GLY
183
A
SER
184
n
183
SER
184
A
ALA
185
n
184
ALA
185
A
SER
186
n
185
SER
186
A
ILE
187
n
186
ILE
187
A
THR
188
n
187
THR
188
A
VAL
189
n
188
VAL
189
A
SER
190
n
189
SER
190
A
author_defined_assembly
1
monomeric
A
IYR
9
3-IODO-TYROSINE
A
IYR
8
TYR
A
IYR
73
3-IODO-TYROSINE
A
IYR
72
TYR
A
IYR
96
3-IODO-TYROSINE
A
IYR
95
TYR
A
TYI
135
3,5-DIIODOTYROSINE
A
TYI
134
TYR
A
TYI
171
3,5-DIIODOTYROSINE
A
TYI
170
TYR
A
IYR
179
3-IODO-TYROSINE
A
IYR
178
TYR
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
ASN
10
A
N
ASN
9
A
O
TYR
13
A
O
TYR
12
A
N
PHE
14
A
N
PHE
13
A
O
GLY
50
A
O
GLY
49
A
N
TRP
51
A
N
TRP
50
A
O
GLN
172
A
O
GLN
171
A
O
ILE
173
A
O
ILE
172
A
N
TYR
77
A
N
TYR
76
A
N
LEU
74
A
N
LEU
73
A
O
ASN
92
A
O
ASN
91
A
N
VAL
90
A
N
VAL
89
A
O
ARG
141
A
O
ARG
140
A
O
PHE
134
A
O
PHE
133
A
N
ARG
122
A
N
ARG
121
A
O
TYR
115
A
O
TYR
114
A
N
VAL
108
A
N
VAL
107
A
N
THR
28
A
N
THR
27
A
O
SER
36
A
O
SER
35
A
N
PHE
35
A
N
PHE
34
A
O
ILE
187
A
O
ILE
186
A
O
SER
182
A
O
SER
181
A
N
ASN
69
A
N
ASN
68
A
N
ILE
60
A
N
ILE
59
A
O
VAL
150
A
O
VAL
149
1
A
ASN
57
-140.53
15.79
1
A
ASN
82
45.70
71.63
1
A
THR
95
80.04
-57.31
1
A
ASP
170
-101.63
-144.31
IYR2.param
protein_IYR2.top
water_rep.param
ion.param
23.0
3.96
0.00
-5.07
-2.93
0.00
-1.04
0.253
0.011
0.209
0.209
2.00
20.10
492
11213
10211
4.8
91.0
RANDOM
761451.20
0.000000
1
RESTRAINED
THROUGHOUT
0.0
MIRAS
Engh & Huber
FLAT MODEL
46.2859
0.455302
0.29
0.23
5.00
0.22
0.12
2.00
20.10
52
1532
1
0
1479
0.008
1.4
26.0
0.76
0.297
0.036
0.236
2.13
69
1429
6
4.6
80.6
17.6
2.00
53.30
2D98
11213
10211
0.0
0.0
1
91.06
2.00
2.13
80.6
refinement
CNS
1.1
data reduction
HKL-2000
data scaling
SCALEPACK
phasing
SHARP
Endo-1,4-beta-xylanase 2 (E.C.3.2.1.8)
Structure of VIL (extra KI/I2 added)-xylanase
1
N
N
2
N
N
3
N
N
A
THR
152
A
THR
151
HELX_P
A
GLN
162
A
GLN
161
1
1
11
covale
1.327
A
GLY
8
A
C
GLY
7
1_555
A
IYR
9
A
N
IYR
8
1_555
covale
1.324
A
IYR
9
A
C
IYR
8
1_555
A
ASN
10
A
N
ASN
9
1_555
covale
1.330
A
SER
72
A
C
SER
71
1_555
A
IYR
73
A
N
IYR
72
1_555
covale
1.326
A
IYR
73
A
C
IYR
72
1_555
A
LEU
74
A
N
LEU
73
1_555
covale
1.329
A
THR
95
A
C
THR
94
1_555
A
IYR
96
A
N
IYR
95
1_555
covale
1.327
A
IYR
96
A
C
IYR
95
1_555
A
ASN
97
A
N
ASN
96
1_555
covale
1.330
A
PHE
134
A
C
PHE
133
1_555
A
TYI
135
A
N
TYI
134
1_555
covale
1.332
A
TYI
135
A
C
TYI
134
1_555
A
GLN
136
A
N
GLN
135
1_555
covale
1.328
A
ASP
170
A
C
ASP
169
1_555
A
TYI
171
A
N
TYI
170
1_555
covale
1.327
A
TYI
171
A
C
TYI
170
1_555
A
GLN
172
A
N
GLN
171
1_555
covale
1.331
A
GLY
178
A
C
GLY
177
1_555
A
IYR
179
A
N
IYR
178
1_555
covale
1.329
A
IYR
179
A
C
IYR
178
1_555
A
PHE
180
A
N
PHE
179
1_555
HYDROLASE
iodo-tyrosine, VAPORIZING IODINE LABELING(VIL), HYDROLASE
A
GLN
52
A
GLN
51
1
A
PRO
53
A
PRO
52
-0.21
A
ASN
82
A
ASN
81
1
A
PRO
83
A
PRO
82
0.28
XYN2_TRIRE
UNP
1
34
P36217
TIQPGTGYNNGYFYSYWNDGHGGVTYTNGPGGQFSVNWSNSGNFVGGKGWQPGTKNKVINFSGSYNPNGNSYLSVYGWSR
NPLIEYYIVENFGTYNPSTGATKLGEVTSDGSVYDIYRTQRVNQPSIIGTATFYQYWSVRRNHRSSGSVNTANHFNAWAQ
QGLTLGTMDYQIVAVEGYFSSGSASITVS
34
222
2D98
2
190
P36217
A
1
1
189
1
TYR
MODIFIED RESIDUE
IYR
9
2D98
A
P36217
UNP
41
8
1
TYR
MODIFIED RESIDUE
IYR
73
2D98
A
P36217
UNP
105
72
1
TYR
MODIFIED RESIDUE
IYR
96
2D98
A
P36217
UNP
128
95
1
TYR
MODIFIED RESIDUE
TYI
135
2D98
A
P36217
UNP
167
134
1
TYR
MODIFIED RESIDUE
TYI
171
2D98
A
P36217
UNP
203
170
1
TYR
MODIFIED RESIDUE
IYR
179
2D98
A
P36217
UNP
211
178
9
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
GLY
6
A
GLY
5
A
ASN
10
A
ASN
9
A
TYR
13
A
TYR
12
A
ASN
19
A
ASN
18
A
ASN
44
A
ASN
43
A
TRP
51
A
TRP
50
A
THR
168
A
THR
167
A
IYR
179
A
IYR
178
A
SER
72
A
SER
71
A
ARG
81
A
ARG
80
A
ILE
85
A
ILE
84
A
GLY
94
A
GLY
93
A
ALA
132
A
ALA
131
A
ARG
141
A
ARG
140
A
SER
113
A
SER
112
A
GLN
125
A
GLN
124
A
THR
103
A
THR
102
A
SER
110
A
SER
109
A
VAL
25
A
VAL
24
A
ASN
29
A
ASN
28
A
GLN
34
A
GLN
33
A
TRP
39
A
TRP
38
A
SER
182
A
SER
181
A
SER
190
A
SER
189
A
VAL
59
A
VAL
58
A
ASN
69
A
ASN
68
A
GLY
148
A
GLY
147
A
ASN
151
A
ASN
150
BINDING SITE FOR RESIDUE IOD A 200
Software
3
A
GLY
24
A
GLY
23
3
1_555
A
THR
26
A
THR
25
3
1_555
A
ASN
38
A
ASN
37
3
1_555
4
P 1 21 1