0.028804
0.000000
0.005344
0.000000
0.013946
0.000000
0.000000
0.000000
0.015327
0.00000
0.00000
0.00000
Sooriyaarachchi, S.
Ubhayasekera, W.
Mowbray, S.L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.00
100.51
90.00
34.718
71.706
66.356
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
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
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
N
N
237
S
C
N
238
N
C
N
239
N
O
N
240
N
C
Y
241
N
C
Y
242
N
C
Y
243
N
C
Y
244
N
C
Y
245
N
C
Y
246
N
C
N
247
N
O
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
H
N
259
N
N
N
260
S
C
N
261
N
C
N
262
N
O
N
263
N
C
N
264
N
C
N
265
N
C
N
266
N
O
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
H
N
275
N
H
N
276
N
N
N
277
S
C
N
278
N
C
N
279
N
O
N
280
N
C
N
281
N
O
N
282
N
O
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
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
R
C
N
295
N
O
N
296
N
C
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
H
N
306
N
H
N
307
N
N
N
308
S
C
N
309
N
C
N
310
N
O
N
311
N
C
Y
312
N
C
Y
313
N
C
Y
314
N
C
Y
315
N
N
Y
316
N
C
Y
317
N
C
Y
318
N
C
Y
319
N
C
Y
320
N
C
N
321
N
O
N
322
N
H
N
323
N
H
N
324
N
H
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
C
Y
343
N
C
Y
344
N
C
N
345
N
O
N
346
N
O
N
347
N
H
N
348
N
H
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
N
N
359
S
C
N
360
N
C
N
361
N
O
N
362
N
C
N
363
N
C
N
364
N
C
N
365
N
O
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
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
O
N
378
R
C
N
379
R
C
N
380
S
C
N
381
R
C
N
382
N
C
N
383
N
O
N
384
N
O
N
385
N
O
N
386
N
O
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
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
doub
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
Y
235
N
doub
Y
236
N
sing
Y
237
N
sing
N
238
N
sing
Y
239
N
doub
N
240
N
sing
Y
241
N
doub
N
242
N
sing
Y
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
sing
N
252
N
sing
N
253
N
doub
N
254
N
sing
N
255
N
sing
N
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
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
doub
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
sing
N
297
N
sing
N
298
N
sing
N
299
N
doub
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
Y
304
N
doub
Y
305
N
sing
Y
306
N
sing
N
307
N
sing
Y
308
N
doub
Y
309
N
sing
Y
310
N
sing
N
311
N
sing
Y
312
N
sing
Y
313
N
doub
N
314
N
sing
Y
315
N
doub
N
316
N
sing
Y
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
sing
N
325
N
sing
N
326
N
sing
N
327
N
doub
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
Y
332
N
doub
Y
333
N
sing
Y
334
N
sing
N
335
N
sing
Y
336
N
doub
N
337
N
sing
Y
338
N
doub
N
339
N
sing
Y
340
N
sing
N
341
N
sing
N
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
doub
N
352
N
sing
N
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
sing
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
402
657
668
10.1016/j.jmb.2010.07.038
20678502
Conformational changes and ligand recognition of Escherichia coli D-xylose binding protein revealed
2010
10.2210/pdb3m9x/pdb
pdb_00003m9x
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
2008-06-29
ADSC QUANTUM 210
SINGLE WAVELENGTH
M
x-ray
1
0.9334
1.0
ID14-1
ESRF
0.9334
SYNCHROTRON
ESRF BEAMLINE ID14-1
34134.734
D-xylose-binding periplasmic protein
1
man
polymer
150.130
beta-D-xylopyranose
1
man
non-polymer
18.015
water
89
nat
water
xylose binding protein
no
no
KEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAK
QEGIKVLAYDRMINDADIDFYISFDNEKVGELQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKV
VGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRIAAGTQTMTV
YKPITLLANTAAEIAVELGNGQEPKADTTLNNGLKDVPSRLLTPIDVNKNNIKDTVIKDGFHKESELHHHHHH
KEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAK
QEGIKVLAYDRMINDADIDFYISFDNEKVGELQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKV
VGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRIAAGTQTMTV
YKPITLLANTAAEIAVELGNGQEPKADTTLNNGLKDVPSRLLTPIDVNKNNIKDTVIKDGFHKESELHHHHHH
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
K-12 substr. MG1655
sample
511145
Escherichia coli
562
Escherichia coli
BL21(AI)
plasmid
pEXP-5-CT/TOPO
1
2.44
49.56
VAPOR DIFFUSION, HANGING DROP
7.5
21%(w/v) polyethylene glycol 3350, 0.2M ammonium dihydrogen phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
296
atom_site
chem_comp
entity
pdbx_chem_comp_identifier
pdbx_entity_nonpoly
struct_ref_seq_dif
struct_site
struct_site_gen
chem_comp
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Database references
Atomic model
Data collection
Database references
Derived calculations
Structure summary
Data collection
Database references
Refinement description
Structure summary
1
0
2010-08-18
1
1
2011-07-13
1
2
2014-03-05
2
0
2020-07-29
2
1
2023-11-01
_atom_site.auth_atom_id
_atom_site.label_atom_id
_chem_comp.name
_chem_comp.type
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_struct_ref_seq_dif.details
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
DXylpb
b-D-xylopyranose
b-D-Xylp
Xyl
Open ligand-free crystal structure of xylose binding protein from Escherichia coli
Close liganded xylose binding protein structure from Escherichia coli
RCSB
Y
PDBJ
2010-03-22
REL
REL
XYP
beta-D-xylopyranose
HOH
water
3M9W
PDB entry 3M9W
PDB
experimental model
XYP
400
2
XYP
XYP
400
A
HOH
1
3
HOH
HOH
314
A
HOH
2
3
HOH
HOH
315
A
HOH
3
3
HOH
HOH
316
A
HOH
4
3
HOH
HOH
317
A
HOH
5
3
HOH
HOH
318
A
HOH
6
3
HOH
HOH
319
A
HOH
7
3
HOH
HOH
320
A
HOH
8
3
HOH
HOH
321
A
HOH
9
3
HOH
HOH
322
A
HOH
10
3
HOH
HOH
323
A
HOH
11
3
HOH
HOH
324
A
HOH
12
3
HOH
HOH
325
A
HOH
13
3
HOH
HOH
326
A
HOH
14
3
HOH
HOH
327
A
HOH
15
3
HOH
HOH
328
A
HOH
16
3
HOH
HOH
329
A
HOH
17
3
HOH
HOH
330
A
HOH
18
3
HOH
HOH
331
A
HOH
19
3
HOH
HOH
332
A
HOH
20
3
HOH
HOH
333
A
HOH
21
3
HOH
HOH
334
A
HOH
22
3
HOH
HOH
335
A
HOH
23
3
HOH
HOH
336
A
HOH
24
3
HOH
HOH
337
A
HOH
25
3
HOH
HOH
338
A
HOH
26
3
HOH
HOH
339
A
HOH
27
3
HOH
HOH
340
A
HOH
28
3
HOH
HOH
341
A
HOH
29
3
HOH
HOH
342
A
HOH
30
3
HOH
HOH
343
A
HOH
31
3
HOH
HOH
344
A
HOH
32
3
HOH
HOH
345
A
HOH
33
3
HOH
HOH
346
A
HOH
34
3
HOH
HOH
347
A
HOH
35
3
HOH
HOH
348
A
HOH
36
3
HOH
HOH
349
A
HOH
37
3
HOH
HOH
350
A
HOH
38
3
HOH
HOH
351
A
HOH
39
3
HOH
HOH
352
A
HOH
40
3
HOH
HOH
353
A
HOH
41
3
HOH
HOH
354
A
HOH
42
3
HOH
HOH
355
A
HOH
43
3
HOH
HOH
356
A
HOH
44
3
HOH
HOH
357
A
HOH
45
3
HOH
HOH
358
A
HOH
46
3
HOH
HOH
359
A
HOH
47
3
HOH
HOH
360
A
HOH
48
3
HOH
HOH
361
A
HOH
49
3
HOH
HOH
362
A
HOH
50
3
HOH
HOH
363
A
HOH
51
3
HOH
HOH
364
A
HOH
52
3
HOH
HOH
365
A
HOH
53
3
HOH
HOH
366
A
HOH
54
3
HOH
HOH
367
A
HOH
55
3
HOH
HOH
368
A
HOH
56
3
HOH
HOH
369
A
HOH
57
3
HOH
HOH
370
A
HOH
58
3
HOH
HOH
371
A
HOH
59
3
HOH
HOH
372
A
HOH
60
3
HOH
HOH
373
A
HOH
61
3
HOH
HOH
374
A
HOH
62
3
HOH
HOH
375
A
HOH
63
3
HOH
HOH
376
A
HOH
64
3
HOH
HOH
377
A
HOH
65
3
HOH
HOH
378
A
HOH
66
3
HOH
HOH
379
A
HOH
67
3
HOH
HOH
380
A
HOH
68
3
HOH
HOH
381
A
HOH
69
3
HOH
HOH
382
A
HOH
70
3
HOH
HOH
383
A
HOH
71
3
HOH
HOH
384
A
HOH
72
3
HOH
HOH
385
A
HOH
73
3
HOH
HOH
386
A
HOH
74
3
HOH
HOH
387
A
HOH
75
3
HOH
HOH
388
A
HOH
76
3
HOH
HOH
389
A
HOH
77
3
HOH
HOH
390
A
HOH
78
3
HOH
HOH
391
A
HOH
79
3
HOH
HOH
392
A
HOH
80
3
HOH
HOH
393
A
HOH
81
3
HOH
HOH
394
A
HOH
82
3
HOH
HOH
395
A
HOH
83
3
HOH
HOH
396
A
HOH
84
3
HOH
HOH
397
A
HOH
85
3
HOH
HOH
398
A
HOH
86
3
HOH
HOH
399
A
HOH
87
3
HOH
HOH
401
A
HOH
88
3
HOH
HOH
402
A
HOH
89
3
HOH
HOH
403
A
n
1
1
A
n
2
2
A
VAL
3
n
3
VAL
3
A
LYS
4
n
4
LYS
4
A
ILE
5
n
5
ILE
5
A
GLY
6
n
6
GLY
6
A
MET
7
n
7
MET
7
A
ALA
8
n
8
ALA
8
A
ILE
9
n
9
ILE
9
A
ASP
10
n
10
ASP
10
A
ASP
11
n
11
ASP
11
A
LEU
12
n
12
LEU
12
A
ARG
13
n
13
ARG
13
A
LEU
14
n
14
LEU
14
A
GLU
15
n
15
GLU
15
A
ARG
16
n
16
ARG
16
A
TRP
17
n
17
TRP
17
A
GLN
18
n
18
GLN
18
A
LYS
19
n
19
LYS
19
A
ASP
20
n
20
ASP
20
A
ARG
21
n
21
ARG
21
A
ASP
22
n
22
ASP
22
A
ILE
23
n
23
ILE
23
A
PHE
24
n
24
PHE
24
A
VAL
25
n
25
VAL
25
A
LYS
26
n
26
LYS
26
A
LYS
27
n
27
LYS
27
A
ALA
28
n
28
ALA
28
A
GLU
29
n
29
GLU
29
A
SER
30
n
30
SER
30
A
LEU
31
n
31
LEU
31
A
GLY
32
n
32
GLY
32
A
ALA
33
n
33
ALA
33
A
LYS
34
n
34
LYS
34
A
VAL
35
n
35
VAL
35
A
PHE
36
n
36
PHE
36
A
VAL
37
n
37
VAL
37
A
GLN
38
n
38
GLN
38
A
SER
39
n
39
SER
39
A
ALA
40
n
40
ALA
40
A
ASN
41
n
41
ASN
41
A
GLY
42
n
42
GLY
42
A
ASN
43
n
43
ASN
43
A
GLU
44
n
44
GLU
44
A
GLU
45
n
45
GLU
45
A
THR
46
n
46
THR
46
A
GLN
47
n
47
GLN
47
A
MET
48
n
48
MET
48
A
SER
49
n
49
SER
49
A
GLN
50
n
50
GLN
50
A
ILE
51
n
51
ILE
51
A
GLU
52
n
52
GLU
52
A
ASN
53
n
53
ASN
53
A
MET
54
n
54
MET
54
A
ILE
55
n
55
ILE
55
A
ASN
56
n
56
ASN
56
A
ARG
57
n
57
ARG
57
A
GLY
58
n
58
GLY
58
A
VAL
59
n
59
VAL
59
A
ASP
60
n
60
ASP
60
A
VAL
61
n
61
VAL
61
A
LEU
62
n
62
LEU
62
A
VAL
63
n
63
VAL
63
A
ILE
64
n
64
ILE
64
A
ILE
65
n
65
ILE
65
A
PRO
66
n
66
PRO
66
A
TYR
67
n
67
TYR
67
A
ASN
68
n
68
ASN
68
A
GLY
69
n
69
GLY
69
A
GLN
70
n
70
GLN
70
A
VAL
71
n
71
VAL
71
A
LEU
72
n
72
LEU
72
A
SER
73
n
73
SER
73
A
ASN
74
n
74
ASN
74
A
VAL
75
n
75
VAL
75
A
VAL
76
n
76
VAL
76
A
LYS
77
n
77
LYS
77
A
GLU
78
n
78
GLU
78
A
ALA
79
n
79
ALA
79
A
LYS
80
n
80
LYS
80
A
GLN
81
n
81
GLN
81
A
GLU
82
n
82
GLU
82
A
GLY
83
n
83
GLY
83
A
ILE
84
n
84
ILE
84
A
LYS
85
n
85
LYS
85
A
VAL
86
n
86
VAL
86
A
LEU
87
n
87
LEU
87
A
ALA
88
n
88
ALA
88
A
TYR
89
n
89
TYR
89
A
ASP
90
n
90
ASP
90
A
ARG
91
n
91
ARG
91
A
MET
92
n
92
MET
92
A
ILE
93
n
93
ILE
93
A
ASN
94
n
94
ASN
94
A
ASP
95
n
95
ASP
95
A
ALA
96
n
96
ALA
96
A
ASP
97
n
97
ASP
97
A
ILE
98
n
98
ILE
98
A
ASP
99
n
99
ASP
99
A
PHE
100
n
100
PHE
100
A
TYR
101
n
101
TYR
101
A
ILE
102
n
102
ILE
102
A
SER
103
n
103
SER
103
A
PHE
104
n
104
PHE
104
A
ASP
105
n
105
ASP
105
A
ASN
106
n
106
ASN
106
A
GLU
107
n
107
GLU
107
A
LYS
108
n
108
LYS
108
A
VAL
109
n
109
VAL
109
A
GLY
110
n
110
GLY
110
A
GLU
111
n
111
GLU
111
A
LEU
112
n
112
LEU
112
A
GLN
113
n
113
GLN
113
A
ALA
114
n
114
ALA
114
A
LYS
115
n
115
LYS
115
A
ALA
116
n
116
ALA
116
A
LEU
117
n
117
LEU
117
A
VAL
118
n
118
VAL
118
A
ASP
119
n
119
ASP
119
A
ILE
120
n
120
ILE
120
A
VAL
121
n
121
VAL
121
A
PRO
122
n
122
PRO
122
A
GLN
123
n
123
GLN
123
A
GLY
124
n
124
GLY
124
A
ASN
125
n
125
ASN
125
A
TYR
126
n
126
TYR
126
A
PHE
127
n
127
PHE
127
A
LEU
128
n
128
LEU
128
A
MET
129
n
129
MET
129
A
GLY
130
n
130
GLY
130
A
GLY
131
n
131
GLY
131
A
SER
132
n
132
SER
132
A
PRO
133
n
133
PRO
133
A
VAL
134
n
134
VAL
134
A
ASP
135
n
135
ASP
135
A
ASN
136
n
136
ASN
136
A
ASN
137
n
137
ASN
137
A
ALA
138
n
138
ALA
138
A
LYS
139
n
139
LYS
139
A
LEU
140
n
140
LEU
140
A
PHE
141
n
141
PHE
141
A
ARG
142
n
142
ARG
142
A
ALA
143
n
143
ALA
143
A
GLY
144
n
144
GLY
144
A
GLN
145
n
145
GLN
145
A
MET
146
n
146
MET
146
A
LYS
147
n
147
LYS
147
A
VAL
148
n
148
VAL
148
A
LEU
149
n
149
LEU
149
A
LYS
150
n
150
LYS
150
A
PRO
151
n
151
PRO
151
A
TYR
152
n
152
TYR
152
A
VAL
153
n
153
VAL
153
A
ASP
154
n
154
ASP
154
A
SER
155
n
155
SER
155
A
GLY
156
n
156
GLY
156
A
LYS
157
n
157
LYS
157
A
ILE
158
n
158
ILE
158
A
LYS
159
n
159
LYS
159
A
VAL
160
n
160
VAL
160
A
VAL
161
n
161
VAL
161
A
GLY
162
n
162
GLY
162
A
ASP
163
n
163
ASP
163
A
GLN
164
n
164
GLN
164
A
TRP
165
n
165
TRP
165
A
VAL
166
n
166
VAL
166
A
ASP
167
n
167
ASP
167
A
GLY
168
n
168
GLY
168
A
TRP
169
n
169
TRP
169
A
LEU
170
n
170
LEU
170
A
PRO
171
n
171
PRO
171
A
GLU
172
n
172
GLU
172
A
ASN
173
n
173
ASN
173
A
ALA
174
n
174
ALA
174
A
LEU
175
n
175
LEU
175
A
LYS
176
n
176
LYS
176
A
ILE
177
n
177
ILE
177
A
MET
178
n
178
MET
178
A
GLU
179
n
179
GLU
179
A
ASN
180
n
180
ASN
180
A
ALA
181
n
181
ALA
181
A
LEU
182
n
182
LEU
182
A
THR
183
n
183
THR
183
A
ALA
184
n
184
ALA
184
A
ASN
185
n
185
ASN
185
A
ASN
186
n
186
ASN
186
A
ASN
187
n
187
ASN
187
A
LYS
188
n
188
LYS
188
A
ILE
189
n
189
ILE
189
A
ASP
190
n
190
ASP
190
A
ALA
191
n
191
ALA
191
A
VAL
192
n
192
VAL
192
A
VAL
193
n
193
VAL
193
A
ALA
194
n
194
ALA
194
A
SER
195
n
195
SER
195
A
ASN
196
n
196
ASN
196
A
ASP
197
n
197
ASP
197
A
ALA
198
n
198
ALA
198
A
THR
199
n
199
THR
199
A
ALA
200
n
200
ALA
200
A
GLY
201
n
201
GLY
201
A
GLY
202
n
202
GLY
202
A
ALA
203
n
203
ALA
203
A
ILE
204
n
204
ILE
204
A
GLN
205
n
205
GLN
205
A
ALA
206
n
206
ALA
206
A
LEU
207
n
207
LEU
207
A
SER
208
n
208
SER
208
A
ALA
209
n
209
ALA
209
A
GLN
210
n
210
GLN
210
A
GLY
211
n
211
GLY
211
A
LEU
212
n
212
LEU
212
A
SER
213
n
213
SER
213
A
GLY
214
n
214
GLY
214
A
LYS
215
n
215
LYS
215
A
VAL
216
n
216
VAL
216
A
ALA
217
n
217
ALA
217
A
ILE
218
n
218
ILE
218
A
SER
219
n
219
SER
219
A
GLY
220
n
220
GLY
220
A
GLN
221
n
221
GLN
221
A
ASP
222
n
222
ASP
222
A
ALA
223
n
223
ALA
223
A
ASP
224
n
224
ASP
224
A
LEU
225
n
225
LEU
225
A
ALA
226
n
226
ALA
226
A
GLY
227
n
227
GLY
227
A
ILE
228
n
228
ILE
228
A
LYS
229
n
229
LYS
229
A
ARG
230
n
230
ARG
230
A
ILE
231
n
231
ILE
231
A
ALA
232
n
232
ALA
232
A
ALA
233
n
233
ALA
233
A
GLY
234
n
234
GLY
234
A
THR
235
n
235
THR
235
A
GLN
236
n
236
GLN
236
A
THR
237
n
237
THR
237
A
MET
238
n
238
MET
238
A
THR
239
n
239
THR
239
A
VAL
240
n
240
VAL
240
A
TYR
241
n
241
TYR
241
A
LYS
242
n
242
LYS
242
A
PRO
243
n
243
PRO
243
A
ILE
244
n
244
ILE
244
A
THR
245
n
245
THR
245
A
LEU
246
n
246
LEU
246
A
LEU
247
n
247
LEU
247
A
ALA
248
n
248
ALA
248
A
ASN
249
n
249
ASN
249
A
THR
250
n
250
THR
250
A
ALA
251
n
251
ALA
251
A
ALA
252
n
252
ALA
252
A
GLU
253
n
253
GLU
253
A
ILE
254
n
254
ILE
254
A
ALA
255
n
255
ALA
255
A
VAL
256
n
256
VAL
256
A
GLU
257
n
257
GLU
257
A
LEU
258
n
258
LEU
258
A
GLY
259
n
259
GLY
259
A
ASN
260
n
260
ASN
260
A
GLY
261
n
261
GLY
261
A
GLN
262
n
262
GLN
262
A
GLU
263
n
263
GLU
263
A
PRO
264
n
264
PRO
264
A
LYS
265
n
265
LYS
265
A
ALA
266
n
266
ALA
266
A
ASP
267
n
267
ASP
267
A
THR
268
n
268
THR
268
A
THR
269
n
269
THR
269
A
LEU
270
n
270
LEU
270
A
ASN
271
n
271
ASN
271
A
ASN
272
n
272
ASN
272
A
GLY
273
n
273
GLY
273
A
LEU
274
n
274
LEU
274
A
LYS
275
n
275
LYS
275
A
ASP
276
n
276
ASP
276
A
VAL
277
n
277
VAL
277
A
PRO
278
n
278
PRO
278
A
SER
279
n
279
SER
279
A
ARG
280
n
280
ARG
280
A
LEU
281
n
281
LEU
281
A
LEU
282
n
282
LEU
282
A
THR
283
n
283
THR
283
A
PRO
284
n
284
PRO
284
A
ILE
285
n
285
ILE
285
A
ASP
286
n
286
ASP
286
A
VAL
287
n
287
VAL
287
A
ASN
288
n
288
ASN
288
A
LYS
289
n
289
LYS
289
A
ASN
290
n
290
ASN
290
A
ASN
291
n
291
ASN
291
A
ILE
292
n
292
ILE
292
A
LYS
293
n
293
LYS
293
A
ASP
294
n
294
ASP
294
A
THR
295
n
295
THR
295
A
VAL
296
n
296
VAL
296
A
ILE
297
n
297
ILE
297
A
LYS
298
n
298
LYS
298
A
ASP
299
n
299
ASP
299
A
GLY
300
n
300
GLY
300
A
PHE
301
n
301
PHE
301
A
HIS
302
n
302
HIS
302
A
LYS
303
n
303
LYS
303
A
GLU
304
n
304
GLU
304
A
SER
305
n
305
SER
305
A
GLU
306
n
306
GLU
306
A
LEU
307
n
307
LEU
307
A
n
308
308
A
n
309
309
A
n
310
310
A
n
311
311
A
n
312
312
A
n
313
313
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
34
A
O
LYS
34
A
N
ILE
5
A
N
ILE
5
A
N
GLY
6
A
N
GLY
6
A
O
VAL
63
A
O
VAL
63
A
N
LEU
62
A
N
LEU
62
A
O
LYS
85
A
O
LYS
85
A
N
ALA
88
A
N
ALA
88
A
O
PHE
100
A
O
PHE
100
A
N
SER
103
A
N
SER
103
A
O
LEU
282
A
O
LEU
282
A
O
VAL
277
A
O
VAL
277
A
N
LEU
270
A
N
LEU
270
A
O
VAL
161
A
O
VAL
161
A
N
TYR
126
A
N
TYR
126
A
N
PHE
127
A
N
PHE
127
A
O
VAL
193
A
O
VAL
193
A
N
VAL
192
A
N
VAL
192
A
O
ALA
217
A
O
ALA
217
A
N
TYR
241
A
N
TYR
241
A
O
ILE
285
A
O
ILE
285
1
A
LYS
1
A
LYS
1
1
Y
1
A
GLU
2
A
GLU
2
1
Y
1
A
HIS
308
A
HIS
308
1
Y
1
A
HIS
309
A
HIS
309
1
Y
1
A
HIS
310
A
HIS
310
1
Y
1
A
HIS
311
A
HIS
311
1
Y
1
A
HIS
312
A
HIS
312
1
Y
1
A
HIS
313
A
HIS
313
1
Y
1
A
VAL
71
-147.08
39.96
1
A
ASP
90
68.58
-46.17
1
A
ASP
97
-92.66
55.84
1
A
ASP
222
105.38
-30.05
1
A
ASN
260
-96.74
31.68
1
A
LEU
274
-161.91
-32.76
1
A
THR
295
-108.75
-81.49
26.790
0.10
0.00
0.61
-0.67
0.00
0.80
0.934
0.901
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.25573
0.19679
0.19979
2.20
30.00
696
13126
5.0
84.46
6.795
0.172
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.390
0.260
0.80
0.80
1.40
PDB entry 3M9W
MAXIMUM LIKELIHOOD
MASK
2.20
30.00
89
2417
10
0
2318
0.017
0.022
2356
1.633
1.970
3186
5.560
5.000
304
38.298
26.827
104
18.183
15.000
430
18.410
15.000
8
0.114
0.200
373
0.007
0.021
1741
0.914
1.500
1508
1.686
2.000
2422
2.513
3.000
848
4.143
4.500
764
0.337
0.269
2.257
38
623
20
54.58
2.1
30
3M9X
14880
0.079
1
0.363
2.1
2.21
2.2
1
data collection
MxCuBE
phasing
MOLREP
refinement
REFMAC
5.5.0072
data reduction
MOSFLM
data scaling
SCALA
Open liganded crystal structure of xylose binding protein from Escherichia coli
1
N
N
2
N
N
3
N
N
A
TRP
17
A
TRP
17
HELX_P
A
LEU
31
A
LEU
31
1
1
15
A
ASN
43
A
ASN
43
HELX_P
A
GLY
58
A
GLY
58
1
2
16
A
LEU
72
A
LEU
72
HELX_P
A
GLU
82
A
GLU
82
1
3
11
A
ASP
105
A
ASP
105
HELX_P
A
ASP
119
A
ASP
119
1
4
15
A
ASP
135
A
ASP
135
HELX_P
A
SER
155
A
SER
155
1
5
21
A
ASP
167
A
ASP
167
HELX_P
A
TRP
169
A
TRP
169
5
6
3
A
LEU
170
A
LEU
170
HELX_P
A
ASN
185
A
ASN
185
1
7
16
A
ASN
196
A
ASN
196
HELX_P
A
ALA
209
A
ALA
209
1
8
14
A
ASP
224
A
ASP
224
HELX_P
A
ALA
233
A
ALA
233
1
9
10
A
PRO
243
A
PRO
243
HELX_P
A
ASN
260
A
ASN
260
1
10
18
A
LYS
303
A
LYS
303
HELX_P
A
LEU
307
A
LEU
307
5
11
5
SUGAR BINDING PROTEIN
xylose binding protein, xylose, conformational changes, SUGAR BINDING PROTEIN
XYLF_ECOLI
UNP
1
24
P37387
KEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAK
QEGIKVLAYDRMINDADIDFYISFDNEKVGELQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKV
VGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRIAAGTQTMTV
YKPITLLANTAAEIAVELGNGQEPKADTTLNNGLKDVPSRLLTPIDVNKNNIKDTVIKDGFHKESEL
24
330
3M9X
1
307
P37387
A
1
1
307
1
expression tag
HIS
308
3M9X
A
P37387
UNP
308
1
expression tag
HIS
309
3M9X
A
P37387
UNP
309
1
expression tag
HIS
310
3M9X
A
P37387
UNP
310
1
expression tag
HIS
311
3M9X
A
P37387
UNP
311
1
expression tag
HIS
312
3M9X
A
P37387
UNP
312
1
expression tag
HIS
313
3M9X
A
P37387
UNP
313
7
4
2
parallel
parallel
parallel
parallel
parallel
anti-parallel
parallel
parallel
parallel
anti-parallel
A
LYS
34
A
LYS
34
A
SER
39
A
SER
39
A
LYS
4
A
LYS
4
A
ILE
9
A
ILE
9
A
VAL
61
A
VAL
61
A
ILE
65
A
ILE
65
A
LYS
85
A
LYS
85
A
TYR
89
A
TYR
89
A
PHE
100
A
PHE
100
A
PHE
104
A
PHE
104
A
ASP
276
A
ASP
276
A
LEU
282
A
LEU
282
A
THR
268
A
THR
268
A
ASN
271
A
ASN
271
A
ILE
158
A
ILE
158
A
TRP
165
A
TRP
165
A
GLY
124
A
GLY
124
A
GLY
130
A
GLY
130
A
ALA
191
A
ALA
191
A
ALA
194
A
ALA
194
A
ALA
217
A
ALA
217
A
ILE
218
A
ILE
218
A
THR
239
A
THR
239
A
TYR
241
A
TYR
241
A
ILE
285
A
ILE
285
A
VAL
287
A
VAL
287
4
P 1 21 1