0.014853
0.008575
0.000000
0.000000
0.017151
0.000000
0.000000
0.000000
0.006046
0.00000
0.00000
0.00000
Vandermarliere, E.
Rombouts, S.
Strelkov, S.V.
Delcour, J.A.
Courtin, C.M.
Rabijns, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
67.326
67.326
165.401
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
Na 1
22.990
SODIUM ION
non-polymer
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
C5 H10 O5
150.130
beta-D-xylopyranose
beta-D-xylose; D-xylose; xylose
D-saccharide, beta 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
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
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
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
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
NA
N
251
N
N
N
252
S
C
N
253
N
C
N
254
N
O
N
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
Y
261
N
C
N
262
N
O
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
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
N
N
275
S
C
N
276
N
C
N
277
N
O
N
278
N
C
N
279
N
C
N
280
N
C
N
281
N
O
N
282
N
H
N
283
N
H
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
N
N
292
S
C
N
293
N
C
N
294
N
O
N
295
N
C
N
296
N
O
N
297
N
O
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
N
N
306
S
C
N
307
N
C
N
308
N
O
N
309
R
C
N
310
N
O
N
311
N
C
N
312
N
O
N
313
N
H
N
314
N
H
N
315
N
H
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
N
N
323
S
C
N
324
N
C
N
325
N
O
N
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
C
Y
330
N
N
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
C
Y
335
N
C
N
336
N
O
N
337
N
H
N
338
N
H
N
339
N
H
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
C
Y
358
N
C
Y
359
N
C
N
360
N
O
N
361
N
O
N
362
N
H
N
363
N
H
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
N
N
374
S
C
N
375
N
C
N
376
N
O
N
377
N
C
N
378
N
C
N
379
N
C
N
380
N
O
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
O
N
393
R
C
N
394
R
C
N
395
S
C
N
396
R
C
N
397
N
C
N
398
N
O
N
399
N
O
N
400
N
O
N
401
N
O
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
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
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
doub
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
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
doub
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
sing
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
doub
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
sing
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
doub
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
sing
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
doub
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
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
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
doub
N
267
N
sing
N
268
N
sing
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
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
doub
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
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
doub
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
Y
317
N
doub
Y
318
N
sing
Y
319
N
sing
N
320
N
sing
Y
321
N
doub
Y
322
N
sing
Y
323
N
sing
N
324
N
sing
Y
325
N
sing
Y
326
N
doub
N
327
N
sing
Y
328
N
doub
N
329
N
sing
Y
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
doub
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
Y
345
N
doub
Y
346
N
sing
Y
347
N
sing
N
348
N
sing
Y
349
N
doub
N
350
N
sing
Y
351
N
doub
N
352
N
sing
Y
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
doub
N
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
sing
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
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
UK
Biochem.J.
BIJOAK
0043
0264-6021
410
71
79
10.1042/BJ20071128
17983355
Crystallographic analysis shows substrate binding at the -3 to +1 active-site subsites and at the surface of glycoside hydrolase family 11 endo-1,4-beta-xylanases.
2008
10.2210/pdb2qz2/pdb
pdb_00002qz2
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
2006-11-22
MAR CCD 165 mm
Fixed exit double crystal Si [111], horizontally focussing
SINGLE WAVELENGTH
M
x-ray
1
0.9918
1.0
BW7A
EMBL/DESY, HAMBURG
0.9918
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE BW7A
19803.889
Endo-1,4-beta-xylanase I
3.2.1.8
E170A
1
man
polymer
282.245
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose
1
man
branched
546.474
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose
1
man
branched
22.990
SODIUM ION
1
syn
non-polymer
18.015
water
37
nat
water
Xylanase I, 1,4- beta-D-xylan xylanohydrolase I
4beta-beta-xylobiose
no
no
SAGINYVQNYNGNLGDFTYDESAGTFSMYWEDGVSSDFVVGLGWTTGSSNAITYSAEYSASGSSSYLAVYGWVNYPQAEY
YIVEDYGDYNPCSSATSLGTVYSDGSTYQVCTDTRTNEPSITGTSTFTQYFSVRESTRTSGTVTVANHFNFWAQHGFGNS
DFNYQVVAVAAWSGAGSASVTISS
SAGINYVQNYNGNLGDFTYDESAGTFSMYWEDGVSSDFVVGLGWTTGSSNAITYSAEYSASGSSSYLAVYGWVNYPQAEY
YIVEDYGDYNPCSSATSLGTVYSDGSTYQVCTDTRTNEPSITGTSTFTQYFSVRESTRTSGTVTVANHFNFWAQHGFGNS
DFNYQVVAVAAWSGAGSASVTISS
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
sample
5061
Aspergillus niger
4922
Pichia pastoris
1
2.73
54.96
VAPOR DIFFUSION, HANGING DROP
7.5
1.6M ammonium sulphate, 0.1M HEPES pH 7.5, 0.1 M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K
277
atom_site
atom_site_anisotrop
chem_comp
diffrn_source
entity
entity_name_com
pdbx_branch_scheme
pdbx_chem_comp_identifier
pdbx_entity_branch
pdbx_entity_branch_descriptor
pdbx_entity_branch_link
pdbx_entity_branch_list
pdbx_entity_nonpoly
pdbx_molecule_features
pdbx_nonpoly_scheme
pdbx_struct_assembly_gen
pdbx_validate_close_contact
struct_asym
struct_conn
struct_site
struct_site_gen
chem_comp
database_2
struct_conn
struct_ref_seq_dif
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Advisory
Atomic model
Data collection
Derived calculations
Structure summary
Database references
Derived calculations
Structure summary
Data collection
Refinement description
1
0
2007-12-25
1
1
2011-07-13
2
0
2020-07-29
2
1
2021-11-10
2
2
2023-10-25
_atom_site.B_iso_or_equiv
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.auth_seq_id
_atom_site.label_asym_id
_atom_site.label_atom_id
_atom_site.label_entity_id
_atom_site.type_symbol
_atom_site_anisotrop.U[1][1]
_atom_site_anisotrop.U[1][2]
_atom_site_anisotrop.U[1][3]
_atom_site_anisotrop.U[2][2]
_atom_site_anisotrop.U[2][3]
_atom_site_anisotrop.U[3][3]
_atom_site_anisotrop.pdbx_auth_asym_id
_atom_site_anisotrop.pdbx_auth_atom_id
_atom_site_anisotrop.pdbx_auth_seq_id
_atom_site_anisotrop.pdbx_label_asym_id
_atom_site_anisotrop.pdbx_label_atom_id
_atom_site_anisotrop.type_symbol
_chem_comp.name
_chem_comp.type
_diffrn_source.pdbx_synchrotron_site
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_validate_close_contact.auth_asym_id_1
_pdbx_validate_close_contact.auth_asym_id_2
_pdbx_validate_close_contact.auth_atom_id_1
_pdbx_validate_close_contact.auth_atom_id_2
_pdbx_validate_close_contact.auth_seq_id_1
_pdbx_validate_close_contact.auth_seq_id_2
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
X
XYP
1136
n
B
XYP
1
X
XYP
1135
n
B
XYP
2
C
XYP
1137
n
C
XYP
1
C
XYP
1138
n
C
XYP
2
C
XYP
1139
n
C
XYP
3
C
XYP
1140
n
C
XYP
4
DXylpb
b-D-xylopyranose
b-D-Xylp
Xyl
RCSB
Y
PDBJ
2007-08-16
REL
REL
oligosaccharide
oligosaccharide
DXylpb1-4DXylpb1-ROH
2
GMML
1.0
Glycam Condensed Sequence
WURCS=2.0/1,2,1/[a212h-1b_1-5]/1-1/a4-b1
2
PDB2Glycan
1.1.0
WURCS
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}
2
PDB-CARE
LINUCS
DXylpb1-4DXylpb1-4DXylpb1-4DXylpb1-ROH
3
GMML
1.0
Glycam Condensed Sequence
WURCS=2.0/1,4,3/[a212h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1
3
PDB2Glycan
1.1.0
WURCS
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}}
3
PDB-CARE
LINUCS
C1
O4
XYP
XYP
2
1
2
O1
HO4
sing
C1
O4
XYP
XYP
2
1
3
O1
HO4
sing
C1
O4
XYP
XYP
3
2
3
O1
HO4
sing
C1
O4
XYP
XYP
4
3
3
O1
HO4
sing
n
n
n
n
n
n
NA
SODIUM ION
HOH
water
THE AUTHORS BELIEVE THAT THESE RESIDUES ARE CORRECT AND
CONFIRM THAT THE ELECTRON DENSITY SHOWS CLEAR EVIDENCE FOR
THESE RESIDUES.
1UKR
PDB
experimental model
Metabolism
oligosaccharide
4beta-beta-xylobiose
Oligosaccharide
NA
1
4
NA
NA
1141
A
HOH
2
5
HOH
HOH
1142
A
HOH
3
5
HOH
HOH
1143
A
HOH
4
5
HOH
HOH
1144
A
HOH
5
5
HOH
HOH
1145
A
HOH
6
5
HOH
HOH
1146
A
HOH
7
5
HOH
HOH
1147
A
HOH
8
5
HOH
HOH
1148
A
HOH
9
5
HOH
HOH
1149
A
HOH
10
5
HOH
HOH
1150
A
HOH
11
5
HOH
HOH
1151
A
HOH
12
5
HOH
HOH
1152
A
HOH
14
5
HOH
HOH
1153
A
HOH
15
5
HOH
HOH
1154
A
HOH
16
5
HOH
HOH
1155
A
HOH
17
5
HOH
HOH
1156
A
HOH
18
5
HOH
HOH
1157
A
HOH
19
5
HOH
HOH
1158
A
HOH
20
5
HOH
HOH
1159
A
HOH
21
5
HOH
HOH
1160
A
HOH
22
5
HOH
HOH
1161
A
HOH
23
5
HOH
HOH
1162
A
HOH
24
5
HOH
HOH
1163
A
HOH
25
5
HOH
HOH
1164
A
HOH
26
5
HOH
HOH
1165
A
HOH
27
5
HOH
HOH
1166
A
HOH
29
5
HOH
HOH
1167
A
HOH
30
5
HOH
HOH
1168
A
HOH
31
5
HOH
HOH
1169
A
HOH
32
5
HOH
HOH
1170
A
HOH
33
5
HOH
HOH
1171
A
HOH
34
5
HOH
HOH
1172
A
HOH
35
5
HOH
HOH
1173
A
HOH
36
5
HOH
HOH
1174
A
HOH
37
5
HOH
HOH
1175
A
HOH
38
5
HOH
HOH
1176
A
HOH
39
5
HOH
HOH
1177
A
HOH
40
5
HOH
HOH
1178
A
SER
1
n
1
SER
1
A
ALA
2
n
2
ALA
2
A
GLY
3
n
3
GLY
3
A
ILE
4
n
4
ILE
4
A
ASN
5
n
5
ASN
5
A
TYR
6
n
6
TYR
6
A
VAL
7
n
7
VAL
7
A
GLN
8
n
8
GLN
8
A
ASN
9
n
9
ASN
9
A
TYR
10
n
10
TYR
10
A
ASN
11
n
11
ASN
11
A
GLY
12
n
12
GLY
12
A
ASN
13
n
13
ASN
13
A
LEU
14
n
14
LEU
14
A
GLY
15
n
15
GLY
15
A
ASP
16
n
16
ASP
16
A
PHE
17
n
17
PHE
17
A
THR
18
n
18
THR
18
A
TYR
19
n
19
TYR
19
A
ASP
20
n
20
ASP
20
A
GLU
21
n
21
GLU
21
A
SER
22
n
22
SER
22
A
ALA
23
n
23
ALA
23
A
GLY
24
n
24
GLY
24
A
THR
25
n
25
THR
25
A
PHE
26
n
26
PHE
26
A
SER
27
n
27
SER
27
A
MET
28
n
28
MET
28
A
TYR
29
n
29
TYR
29
A
TRP
30
n
30
TRP
30
A
GLU
31
n
31
GLU
31
A
ASP
32
n
32
ASP
32
A
GLY
33
n
33
GLY
33
A
VAL
34
n
34
VAL
34
A
SER
35
n
35
SER
35
A
SER
36
n
36
SER
36
A
ASP
37
n
37
ASP
37
A
PHE
38
n
38
PHE
38
A
VAL
39
n
39
VAL
39
A
VAL
40
n
40
VAL
40
A
GLY
41
n
41
GLY
41
A
LEU
42
n
42
LEU
42
A
GLY
43
n
43
GLY
43
A
TRP
44
n
44
TRP
44
A
THR
45
n
45
THR
45
A
THR
46
n
46
THR
46
A
GLY
47
n
47
GLY
47
A
SER
48
n
48
SER
48
A
SER
49
n
49
SER
49
A
ASN
50
n
50
ASN
50
A
ALA
51
n
51
ALA
51
A
ILE
52
n
52
ILE
52
A
THR
53
n
53
THR
53
A
TYR
54
n
54
TYR
54
A
SER
55
n
55
SER
55
A
ALA
56
n
56
ALA
56
A
GLU
57
n
57
GLU
57
A
TYR
58
n
58
TYR
58
A
SER
59
n
59
SER
59
A
ALA
60
n
60
ALA
60
A
SER
61
n
61
SER
61
A
GLY
62
n
62
GLY
62
A
SER
63
n
63
SER
63
A
SER
64
n
64
SER
64
A
SER
65
n
65
SER
65
A
TYR
66
n
66
TYR
66
A
LEU
67
n
67
LEU
67
A
ALA
68
n
68
ALA
68
A
VAL
69
n
69
VAL
69
A
TYR
70
n
70
TYR
70
A
GLY
71
n
71
GLY
71
A
TRP
72
n
72
TRP
72
A
VAL
73
n
73
VAL
73
A
ASN
74
n
74
ASN
74
A
TYR
75
n
75
TYR
75
A
PRO
76
n
76
PRO
76
A
GLN
77
n
77
GLN
77
A
ALA
78
n
78
ALA
78
A
GLU
79
n
79
GLU
79
A
TYR
80
n
80
TYR
80
A
TYR
81
n
81
TYR
81
A
ILE
82
n
82
ILE
82
A
VAL
83
n
83
VAL
83
A
GLU
84
n
84
GLU
84
A
ASP
85
n
85
ASP
85
A
TYR
86
n
86
TYR
86
A
GLY
87
n
87
GLY
87
A
ASP
88
n
88
ASP
88
A
TYR
89
n
89
TYR
89
A
ASN
90
n
90
ASN
90
A
PRO
91
n
91
PRO
91
A
CYS
92
n
92
CYS
92
A
SER
93
n
93
SER
93
A
SER
94
n
94
SER
94
A
ALA
95
n
95
ALA
95
A
THR
96
n
96
THR
96
A
SER
97
n
97
SER
97
A
LEU
98
n
98
LEU
98
A
GLY
99
n
99
GLY
99
A
THR
100
n
100
THR
100
A
VAL
101
n
101
VAL
101
A
TYR
102
n
102
TYR
102
A
SER
103
n
103
SER
103
A
ASP
104
n
104
ASP
104
A
GLY
105
n
105
GLY
105
A
SER
106
n
106
SER
106
A
THR
107
n
107
THR
107
A
TYR
108
n
108
TYR
108
A
GLN
109
n
109
GLN
109
A
VAL
110
n
110
VAL
110
A
CYS
111
n
111
CYS
111
A
THR
112
n
112
THR
112
A
ASP
113
n
113
ASP
113
A
THR
114
n
114
THR
114
A
ARG
115
n
115
ARG
115
A
THR
116
n
116
THR
116
A
ASN
117
n
117
ASN
117
A
GLU
118
n
118
GLU
118
A
PRO
119
n
119
PRO
119
A
SER
120
n
120
SER
120
A
ILE
121
n
121
ILE
121
A
THR
122
n
122
THR
122
A
GLY
123
n
123
GLY
123
A
THR
124
n
124
THR
124
A
SER
125
n
125
SER
125
A
THR
126
n
126
THR
126
A
PHE
127
n
127
PHE
127
A
THR
128
n
128
THR
128
A
GLN
129
n
129
GLN
129
A
TYR
130
n
130
TYR
130
A
PHE
131
n
131
PHE
131
A
SER
132
n
132
SER
132
A
VAL
133
n
133
VAL
133
A
ARG
134
n
134
ARG
134
A
GLU
135
n
135
GLU
135
A
SER
136
n
136
SER
136
A
THR
137
n
137
THR
137
A
ARG
138
n
138
ARG
138
A
THR
139
n
139
THR
139
A
SER
140
n
140
SER
140
A
GLY
141
n
141
GLY
141
A
THR
142
n
142
THR
142
A
VAL
143
n
143
VAL
143
A
THR
144
n
144
THR
144
A
VAL
145
n
145
VAL
145
A
ALA
146
n
146
ALA
146
A
ASN
147
n
147
ASN
147
A
HIS
148
n
148
HIS
148
A
PHE
149
n
149
PHE
149
A
ASN
150
n
150
ASN
150
A
PHE
151
n
151
PHE
151
A
TRP
152
n
152
TRP
152
A
ALA
153
n
153
ALA
153
A
GLN
154
n
154
GLN
154
A
HIS
155
n
155
HIS
155
A
GLY
156
n
156
GLY
156
A
PHE
157
n
157
PHE
157
A
GLY
158
n
158
GLY
158
A
ASN
159
n
159
ASN
159
A
SER
160
n
160
SER
160
A
ASP
161
n
161
ASP
161
A
PHE
162
n
162
PHE
162
A
ASN
163
n
163
ASN
163
A
TYR
164
n
164
TYR
164
A
GLN
165
n
165
GLN
165
A
VAL
166
n
166
VAL
166
A
VAL
167
n
167
VAL
167
A
ALA
168
n
168
ALA
168
A
VAL
169
n
169
VAL
169
A
ALA
170
n
170
ALA
170
A
ALA
171
n
171
ALA
171
A
TRP
172
n
172
TRP
172
A
SER
173
n
173
SER
173
A
GLY
174
n
174
GLY
174
A
ALA
175
n
175
ALA
175
A
GLY
176
n
176
GLY
176
A
SER
177
n
177
SER
177
A
ALA
178
n
178
ALA
178
A
SER
179
n
179
SER
179
A
VAL
180
n
180
VAL
180
A
THR
181
n
181
THR
181
A
ILE
182
n
182
ILE
182
A
SER
183
n
183
SER
183
A
n
184
184
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
N
GLN
8
A
N
GLN
8
A
O
GLY
41
A
O
GLY
41
A
N
VAL
40
A
N
VAL
40
A
O
VAL
169
A
O
VAL
169
A
O
VAL
166
A
O
VAL
166
A
N
TYR
70
A
N
TYR
70
A
N
LEU
67
A
N
LEU
67
A
O
ASP
85
A
O
ASP
85
A
N
GLU
79
A
N
GLU
79
A
O
TYR
130
A
O
TYR
130
A
O
VAL
133
A
O
VAL
133
A
N
GLN
109
A
N
GLN
109
A
O
VAL
110
A
O
VAL
110
A
N
LEU
98
A
N
LEU
98
A
N
THR
18
A
N
THR
18
A
O
SER
27
A
O
SER
27
A
N
PHE
26
A
N
PHE
26
A
O
VAL
180
A
O
VAL
180
A
O
THR
181
A
O
THR
181
A
N
SER
55
A
N
SER
55
A
N
ILE
52
A
N
ILE
52
A
O
VAL
143
A
O
VAL
143
1
A
SER
184
A
SER
184
1
Y
1
C
C
O4
O5
XYP
XYP
1
2
1.67
1
22.92
2.20
113.40
136.32
A
A
A
CA
CB
CG
GLU
GLU
GLU
31
31
31
B
B
B
N
1
24.12
2.70
114.20
138.32
A
A
A
CB
CG
CD
GLU
GLU
GLU
31
31
31
B
B
B
N
1
A
A
CD
OE1
GLU
GLU
31
31
-0.082
0.011
1.252
1.170
B
B
N
1
A
A
CA
CB
ALA
ALA
153
153
-0.141
0.021
1.520
1.379
N
1
A
SER
36
-107.81
-165.20
1
A
ASN
163
-96.24
-145.06
23.812
0.04
0.71
0.00
0.04
0.00
-0.06
0.904
0.852
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.27678
0.22120
0.22632
2.80
19.48
542
5220
5219
9.4
97.31
32.331
0.294
RANDOM
1
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
0.433
0.80
0.80
1.20
1UKR
MAXIMUM LIKELIHOOD
MASK
2.80
19.48
37
1496
57
0
1402
0.006
0.021
1501
1.005
1.933
2057
6.212
5.000
182
35.048
24.286
70
13.951
15.000
175
31.141
15.000
3
0.064
0.200
231
0.002
0.020
1158
0.177
0.200
655
0.310
0.200
1010
0.118
0.200
63
0.008
0.200
1
0.139
0.200
15
0.168
0.200
3
0.312
1.500
899
0.564
2.000
1441
0.356
3.000
644
0.595
4.500
616
0.333
3.000
1543
0.931
3.000
38
0.267
3.000
1459
0.326
0.265
2.874
36
343
20
95.47
2.8
30
2QZ2
6010
5843
2.0
1.4
0.094
1
13.7
98.2
2.8
2.85
5.3
271
0.302
98.2
refinement
REFMAC
5.2.0019
data collection
MAR345dtb
data reduction
DENZO
data scaling
SCALEPACK
phasing
PHASER
Crystal structure of a glycoside hydrolase family 11 xylanase from Aspergillus niger in complex with xylopentaose
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
A
ASN
11
A
ASN
11
HELX_P
A
GLY
15
A
GLY
15
5
1
5
A
ASN
90
A
ASN
90
HELX_P
A
SER
94
A
SER
94
5
2
5
A
THR
144
A
THR
144
HELX_P
A
ALA
153
A
ALA
153
1
3
10
A
GLN
154
A
GLN
154
HELX_P
A
GLY
156
A
GLY
156
5
4
3
disulf
2.048
A
CYS
92
A
SG
CYS
92
1_555
A
CYS
111
A
SG
CYS
111
1_555
covale
1.432
both
B
XYP
1
B
O4
XYP
1_555
B
XYP
2
B
C1
XYP
1_555
covale
1.229
both
C
XYP
1
C
O4
XYP
1_555
C
XYP
2
C
C1
XYP
1_555
covale
1.554
both
C
XYP
2
C
O4
XYP
1_555
C
XYP
3
C
C1
XYP
1_555
covale
1.599
both
C
XYP
3
C
O4
XYP
1_555
C
XYP
4
C
C1
XYP
1_555
HYDROLASE
glycoside hydrolase, xylanase, Glycosidase, Xylan degradation, hydrolase
A
SER
1
A
SER
1
1
A
ALA
2
A
ALA
2
-8.20
A
ALA
2
A
ALA
2
1
A
GLY
3
A
GLY
3
-0.01
A
TYR
75
A
TYR
75
1
A
PRO
76
A
PRO
76
-7.45
XYN1_ASPNG
UNP
1
28
P55329
SAGINYVQNYNGNLGDFTYDESAGTFSMYWEDGVSSDFVVGLGWTTGSSKAITYSAEYSASGSSSYLAVYGWVNYPQAEY
YIVEDYGDYNPCSSATSLGTVYSDGSTYQVCTDTRTNEPSITGTSTFTQYFSVRESTRTSGTVTVANHFNFWAQHGFGNS
DFNYQVMAVEAWSGAGSASVTISS
28
211
2QZ2
1
184
P55329
A
1
1
184
1
LYS
SEE REMARK 999
ASN
50
2QZ2
A
P55329
UNP
77
50
1
MET
SEE REMARK 999
VAL
167
2QZ2
A
P55329
UNP
194
167
1
GLU
engineered mutation
ALA
170
2QZ2
A
P55329
UNP
197
170
8
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TYR
6
A
TYR
6
A
TYR
10
A
TYR
10
A
PHE
38
A
PHE
38
A
TRP
44
A
TRP
44
A
PHE
162
A
PHE
162
A
GLY
174
A
GLY
174
A
SER
63
A
SER
63
A
VAL
73
A
VAL
73
A
ALA
78
A
ALA
78
A
TYR
86
A
TYR
86
A
GLY
123
A
GLY
123
A
ARG
134
A
ARG
134
A
SER
106
A
SER
106
A
SER
120
A
SER
120
A
THR
96
A
THR
96
A
SER
103
A
SER
103
A
ASP
16
A
ASP
16
A
ASP
20
A
ASP
20
A
THR
25
A
THR
25
A
TRP
30
A
TRP
30
A
GLY
176
A
GLY
176
A
SER
183
A
SER
183
A
ILE
52
A
ILE
52
A
SER
59
A
SER
59
A
SER
140
A
SER
140
A
VAL
143
A
VAL
143
179
P 65 2 2