.028850
.000000
.005337
.000000
.013853
.000000
.000000
.000000
.015334
.00000
.00000
.00000
Sooriyaarachchi, S.
Ubhayasekera, W.
Mowbray, S.L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.00
100.48
90.00
34.663
72.188
66.322
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
O4 P -3
94.971
PHOSPHATE ION
non-polymer
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
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
P
N
260
N
O
N
261
N
O
N
262
N
O
N
263
N
O
N
264
N
N
N
265
S
C
N
266
N
C
N
267
N
O
N
268
N
C
N
269
N
C
N
270
N
C
N
271
N
O
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
N
N
282
S
C
N
283
N
C
N
284
N
O
N
285
N
C
N
286
N
O
N
287
N
O
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
N
N
296
S
C
N
297
N
C
N
298
N
O
N
299
R
C
N
300
N
O
N
301
N
C
N
302
N
O
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
N
N
313
S
C
N
314
N
C
N
315
N
O
N
316
N
C
Y
317
N
C
Y
318
N
C
Y
319
N
C
Y
320
N
N
Y
321
N
C
Y
322
N
C
Y
323
N
C
Y
324
N
C
Y
325
N
C
N
326
N
O
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
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
N
N
340
S
C
N
341
N
C
N
342
N
O
N
343
N
C
Y
344
N
C
Y
345
N
C
Y
346
N
C
Y
347
N
C
Y
348
N
C
Y
349
N
C
N
350
N
O
N
351
N
O
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
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
N
N
364
S
C
N
365
N
C
N
366
N
O
N
367
N
C
N
368
N
C
N
369
N
C
N
370
N
O
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
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
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
doub
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
doub
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
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
doub
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
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
doub
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
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
doub
N
304
N
sing
N
305
N
sing
N
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
doub
Y
313
N
sing
Y
314
N
sing
N
315
N
sing
Y
316
N
sing
Y
317
N
doub
N
318
N
sing
Y
319
N
doub
N
320
N
sing
Y
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
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
doub
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
Y
336
N
doub
Y
337
N
sing
Y
338
N
sing
N
339
N
sing
Y
340
N
doub
N
341
N
sing
Y
342
N
doub
N
343
N
sing
Y
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
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
doub
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
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/pdb3m9w/pdb
pdb_00003m9w
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
2008-03-12
ADSC QUANTUM 315r
SINGLE WAVELENGTH
M
x-ray
1
0.955
1.0
ID14-4
ESRF
0.955
SYNCHROTRON
ESRF BEAMLINE ID14-4
34134.734
D-xylose-binding periplasmic protein
1
man
polymer
94.971
PHOSPHATE ION
1
syn
non-polymer
18.015
water
94
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
2.45
49.79
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
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Database references
Data collection
Database references
Derived calculations
Refinement description
1
0
2010-08-18
1
1
2011-07-13
1
2
2014-03-05
1
3
2023-11-01
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Open liganded xylose binding protein structure from Escherichia coli
Close liganded xylose binding protein structure from Escherichia coli
RCSB
Y
PDBJ
2010-03-22
REL
REL
PO4
PHOSPHATE ION
HOH
water
2IOY
PDB entry 2IOY
PDB
experimental model
PO4
500
2
PO4
PO4
500
A
HOH
7
3
HOH
HOH
314
A
HOH
8
3
HOH
HOH
315
A
HOH
9
3
HOH
HOH
316
A
HOH
10
3
HOH
HOH
317
A
HOH
11
3
HOH
HOH
318
A
HOH
12
3
HOH
HOH
319
A
HOH
13
3
HOH
HOH
320
A
HOH
14
3
HOH
HOH
321
A
HOH
15
3
HOH
HOH
322
A
HOH
16
3
HOH
HOH
323
A
HOH
17
3
HOH
HOH
324
A
HOH
18
3
HOH
HOH
325
A
HOH
19
3
HOH
HOH
326
A
HOH
20
3
HOH
HOH
327
A
HOH
21
3
HOH
HOH
328
A
HOH
22
3
HOH
HOH
329
A
HOH
23
3
HOH
HOH
330
A
HOH
24
3
HOH
HOH
331
A
HOH
25
3
HOH
HOH
332
A
HOH
26
3
HOH
HOH
333
A
HOH
27
3
HOH
HOH
334
A
HOH
28
3
HOH
HOH
335
A
HOH
29
3
HOH
HOH
336
A
HOH
30
3
HOH
HOH
337
A
HOH
31
3
HOH
HOH
338
A
HOH
32
3
HOH
HOH
339
A
HOH
33
3
HOH
HOH
340
A
HOH
34
3
HOH
HOH
341
A
HOH
35
3
HOH
HOH
342
A
HOH
36
3
HOH
HOH
343
A
HOH
37
3
HOH
HOH
344
A
HOH
38
3
HOH
HOH
345
A
HOH
39
3
HOH
HOH
346
A
HOH
40
3
HOH
HOH
347
A
HOH
41
3
HOH
HOH
348
A
HOH
42
3
HOH
HOH
349
A
HOH
43
3
HOH
HOH
350
A
HOH
44
3
HOH
HOH
351
A
HOH
45
3
HOH
HOH
352
A
HOH
46
3
HOH
HOH
353
A
HOH
47
3
HOH
HOH
354
A
HOH
48
3
HOH
HOH
355
A
HOH
49
3
HOH
HOH
356
A
HOH
50
3
HOH
HOH
357
A
HOH
51
3
HOH
HOH
358
A
HOH
52
3
HOH
HOH
359
A
HOH
53
3
HOH
HOH
360
A
HOH
54
3
HOH
HOH
361
A
HOH
55
3
HOH
HOH
362
A
HOH
56
3
HOH
HOH
363
A
HOH
57
3
HOH
HOH
364
A
HOH
58
3
HOH
HOH
365
A
HOH
59
3
HOH
HOH
366
A
HOH
60
3
HOH
HOH
367
A
HOH
61
3
HOH
HOH
368
A
HOH
62
3
HOH
HOH
369
A
HOH
63
3
HOH
HOH
370
A
HOH
64
3
HOH
HOH
371
A
HOH
65
3
HOH
HOH
372
A
HOH
66
3
HOH
HOH
373
A
HOH
67
3
HOH
HOH
374
A
HOH
68
3
HOH
HOH
375
A
HOH
69
3
HOH
HOH
376
A
HOH
70
3
HOH
HOH
377
A
HOH
71
3
HOH
HOH
378
A
HOH
72
3
HOH
HOH
379
A
HOH
73
3
HOH
HOH
380
A
HOH
74
3
HOH
HOH
381
A
HOH
75
3
HOH
HOH
382
A
HOH
76
3
HOH
HOH
383
A
HOH
77
3
HOH
HOH
384
A
HOH
78
3
HOH
HOH
385
A
HOH
79
3
HOH
HOH
386
A
HOH
80
3
HOH
HOH
387
A
HOH
81
3
HOH
HOH
388
A
HOH
82
3
HOH
HOH
389
A
HOH
83
3
HOH
HOH
390
A
HOH
84
3
HOH
HOH
391
A
HOH
85
3
HOH
HOH
392
A
HOH
86
3
HOH
HOH
393
A
HOH
87
3
HOH
HOH
394
A
HOH
88
3
HOH
HOH
395
A
HOH
89
3
HOH
HOH
396
A
HOH
90
3
HOH
HOH
397
A
HOH
91
3
HOH
HOH
398
A
HOH
92
3
HOH
HOH
399
A
HOH
93
3
HOH
HOH
400
A
HOH
94
3
HOH
HOH
401
A
HOH
1
3
HOH
HOH
402
A
HOH
2
3
HOH
HOH
403
A
HOH
3
3
HOH
HOH
404
A
HOH
4
3
HOH
HOH
405
A
HOH
5
3
HOH
HOH
406
A
HOH
6
3
HOH
HOH
407
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
PHE
36
A
O
PHE
36
A
N
MET
7
A
N
MET
7
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
THR
239
A
N
THR
239
A
O
VAL
287
A
O
VAL
287
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
ASP
90
67.83
-36.57
1
A
ASP
163
-168.24
114.71
1
A
TRP
169
56.55
15.04
1
A
ASP
222
109.51
-28.77
1
A
LEU
274
-178.94
-45.44
1
A
THR
295
-117.46
-87.76
29.469
-.31
.00
2.27
-1.08
.00
2.21
.938
.904
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
.26429
.20762
.21032
2.15
20.00
862
16242
5.0
97.41
6.035
.158
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
.278
.225
.80
.80
1.40
PDB entry 2IOY
MAXIMUM LIKELIHOOD
MASK
2.15
20.00
94
2417
5
0
2318
.010
.022
2350
1.223
1.967
3178
4.909
5.000
304
34.602
26.827
104
16.163
15.000
430
21.834
15.000
8
.079
.200
369
.005
.021
1741
.613
1.500
1508
1.139
2.000
2422
1.698
3.000
842
2.835
4.500
756
.300
.250
2.205
71
1181
20
98.82
2.15
20
3M9W
17127
0.084
1
0.372
2.15
2.27
3.4
2518
1
data collection
MxCuBE
phasing
MOLREP
refinement
REFMAC
5.4.0073
data reduction
MOSFLM
data scaling
SCALA
Open ligand-free 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
ARG
57
A
ARG
57
1
2
15
A
LEU
72
A
LEU
72
HELX_P
A
GLN
81
A
GLN
81
1
3
10
A
ASP
105
A
ASP
105
HELX_P
A
VAL
121
A
VAL
121
1
4
17
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
GLY
234
A
GLY
234
1
9
11
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
3M9W
1
307
P37387
A
1
1
307
1
expression tag
HIS
308
3M9W
A
P37387
UNP
308
1
expression tag
HIS
309
3M9W
A
P37387
UNP
309
1
expression tag
HIS
310
3M9W
A
P37387
UNP
310
1
expression tag
HIS
311
3M9W
A
P37387
UNP
311
1
expression tag
HIS
312
3M9W
A
P37387
UNP
312
1
expression tag
HIS
313
3M9W
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
BINDING SITE FOR RESIDUE PO4 A 500
A
PO4
500
Software
4
A
TRP
169
A
TRP
169
4
1_555
A
ASN
196
A
ASN
196
4
1_555
A
GLN
221
A
GLN
221
4
1_555
A
ASP
222
A
ASP
222
4
1_555
4
P 1 21 1