0.00862
0.00498
0.00000
0.00000
0.00996
0.00000
0.00000
0.00000
0.00836
0.00000
0.00000
0.00000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.000
90.000
120.000
115.980
115.980
119.639
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
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
C5 H11 N O2 Se
196.106
n
SELENOMETHIONINE
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
To be published
0353
Crystal structure of transcription regulator from Bacteroides thetaiotaomicron VPI-5482 at 2.15 A resolution
10.2210/pdb1zyb/pdb
pdb_00001zyb
100
1
Double-crystal monochromator (Si 111), toroid
CCD
2005-05-05
ADSC QUANTUM 4
MAD
M
x-ray
1
0.979094
1.0
0.918381
1.0
BL1-5
SSRL
0.979094, 0.918381
SYNCHROTRON
SSRL BEAMLINE BL1-5
27209.520
transcription regulator, CRP family
1
man
polymer
92.094
GLYCEROL
7
syn
non-polymer
18.015
water
187
nat
water
no
yes
(MSE)GSDKIHHHHHH(MSE)ET(MSE)FDTLLQLPLFQGLCHEDFTSILDKVKLHFIKHKAGETIIKSGNPCTQLCFLL
KGEISIVTNAKENIYTVIEQIEAPYLIEPQSLFG(MSE)NTNYASSYVAHTEVHTVCISKAFVLSDLFRYDIFRLNY
(MSE)NIVSNRAQNLYSRLWDEPTLDLKSKIIRFFLSHCEKPQGEKTFKVK(MSE)DDLARCLDDTRLNISKTLNELQDN
GLIELHRKEILIPDAQKLL
MGSDKIHHHHHHMETMFDTLLQLPLFQGLCHEDFTSILDKVKLHFIKHKAGETIIKSGNPCTQLCFLLKGEISIVTNAKE
NIYTVIEQIEAPYLIEPQSLFGMNTNYASSYVAHTEVHTVCISKAFVLSDLFRYDIFRLNYMNIVSNRAQNLYSRLWDEP
TLDLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNELQDNGLIELHRKEILIPDAQKLL
A
358851
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
Bacteroides
Bacteroides thetaiotaomicron
VPI-5482
Escherichia
sample
np_813211.1
226186
Bacteroides thetaiotaomicron
562
Escherichia coli
Plasmid
1
3.86
67.86
4.0M NaFormate, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 273K
273
Joint Center for Structural Genomics
JCSG
PSI, Protein Structure Initiative
software
database_2
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Advisory
Derived calculations
Source and taxonomy
Version format compliance
Refinement description
Database references
Derived calculations
1
0
2005-07-19
1
1
2008-04-30
1
2
2011-07-13
1
3
2017-10-11
1
4
2023-01-25
_software.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
RCSB
Y
RCSB
2005-06-09
REL
REL
GOL
GLYCEROL
HOH
water
GOL
1
2
GOL
GOL
221
A
GOL
2
2
GOL
GOL
222
A
GOL
3
2
GOL
GOL
223
A
GOL
4
2
GOL
GOL
224
A
GOL
5
2
GOL
GOL
225
A
GOL
6
2
GOL
GOL
226
A
GOL
7
2
GOL
GOL
227
A
HOH
8
3
HOH
HOH
228
A
HOH
9
3
HOH
HOH
229
A
HOH
10
3
HOH
HOH
230
A
HOH
11
3
HOH
HOH
231
A
HOH
12
3
HOH
HOH
232
A
HOH
13
3
HOH
HOH
233
A
HOH
14
3
HOH
HOH
234
A
HOH
15
3
HOH
HOH
235
A
HOH
16
3
HOH
HOH
236
A
HOH
17
3
HOH
HOH
237
A
HOH
18
3
HOH
HOH
238
A
HOH
19
3
HOH
HOH
239
A
HOH
20
3
HOH
HOH
240
A
HOH
21
3
HOH
HOH
241
A
HOH
22
3
HOH
HOH
242
A
HOH
23
3
HOH
HOH
243
A
HOH
24
3
HOH
HOH
244
A
HOH
25
3
HOH
HOH
245
A
HOH
26
3
HOH
HOH
246
A
HOH
27
3
HOH
HOH
247
A
HOH
28
3
HOH
HOH
248
A
HOH
29
3
HOH
HOH
249
A
HOH
30
3
HOH
HOH
250
A
HOH
31
3
HOH
HOH
251
A
HOH
32
3
HOH
HOH
252
A
HOH
33
3
HOH
HOH
253
A
HOH
34
3
HOH
HOH
254
A
HOH
35
3
HOH
HOH
255
A
HOH
36
3
HOH
HOH
256
A
HOH
37
3
HOH
HOH
257
A
HOH
38
3
HOH
HOH
258
A
HOH
39
3
HOH
HOH
259
A
HOH
40
3
HOH
HOH
260
A
HOH
41
3
HOH
HOH
261
A
HOH
42
3
HOH
HOH
262
A
HOH
43
3
HOH
HOH
263
A
HOH
44
3
HOH
HOH
264
A
HOH
45
3
HOH
HOH
265
A
HOH
46
3
HOH
HOH
266
A
HOH
47
3
HOH
HOH
267
A
HOH
48
3
HOH
HOH
268
A
HOH
49
3
HOH
HOH
269
A
HOH
50
3
HOH
HOH
270
A
HOH
51
3
HOH
HOH
271
A
HOH
52
3
HOH
HOH
272
A
HOH
53
3
HOH
HOH
273
A
HOH
54
3
HOH
HOH
274
A
HOH
55
3
HOH
HOH
275
A
HOH
56
3
HOH
HOH
276
A
HOH
57
3
HOH
HOH
277
A
HOH
58
3
HOH
HOH
278
A
HOH
59
3
HOH
HOH
279
A
HOH
60
3
HOH
HOH
280
A
HOH
61
3
HOH
HOH
281
A
HOH
62
3
HOH
HOH
282
A
HOH
63
3
HOH
HOH
283
A
HOH
64
3
HOH
HOH
284
A
HOH
65
3
HOH
HOH
285
A
HOH
66
3
HOH
HOH
286
A
HOH
67
3
HOH
HOH
287
A
HOH
68
3
HOH
HOH
288
A
HOH
69
3
HOH
HOH
289
A
HOH
70
3
HOH
HOH
290
A
HOH
71
3
HOH
HOH
291
A
HOH
72
3
HOH
HOH
292
A
HOH
73
3
HOH
HOH
293
A
HOH
74
3
HOH
HOH
294
A
HOH
75
3
HOH
HOH
295
A
HOH
76
3
HOH
HOH
296
A
HOH
77
3
HOH
HOH
297
A
HOH
78
3
HOH
HOH
298
A
HOH
79
3
HOH
HOH
299
A
HOH
80
3
HOH
HOH
300
A
HOH
81
3
HOH
HOH
301
A
HOH
82
3
HOH
HOH
302
A
HOH
83
3
HOH
HOH
303
A
HOH
84
3
HOH
HOH
304
A
HOH
85
3
HOH
HOH
305
A
HOH
86
3
HOH
HOH
306
A
HOH
87
3
HOH
HOH
307
A
HOH
88
3
HOH
HOH
308
A
HOH
89
3
HOH
HOH
309
A
HOH
90
3
HOH
HOH
310
A
HOH
91
3
HOH
HOH
311
A
HOH
92
3
HOH
HOH
312
A
HOH
93
3
HOH
HOH
313
A
HOH
94
3
HOH
HOH
314
A
HOH
95
3
HOH
HOH
315
A
HOH
96
3
HOH
HOH
316
A
HOH
97
3
HOH
HOH
317
A
HOH
98
3
HOH
HOH
318
A
HOH
99
3
HOH
HOH
319
A
HOH
100
3
HOH
HOH
320
A
HOH
101
3
HOH
HOH
321
A
HOH
102
3
HOH
HOH
322
A
HOH
103
3
HOH
HOH
323
A
HOH
104
3
HOH
HOH
324
A
HOH
105
3
HOH
HOH
325
A
HOH
106
3
HOH
HOH
326
A
HOH
107
3
HOH
HOH
327
A
HOH
108
3
HOH
HOH
328
A
HOH
109
3
HOH
HOH
329
A
HOH
110
3
HOH
HOH
330
A
HOH
111
3
HOH
HOH
331
A
HOH
112
3
HOH
HOH
332
A
HOH
113
3
HOH
HOH
333
A
HOH
114
3
HOH
HOH
334
A
HOH
115
3
HOH
HOH
335
A
HOH
116
3
HOH
HOH
336
A
HOH
117
3
HOH
HOH
337
A
HOH
118
3
HOH
HOH
338
A
HOH
119
3
HOH
HOH
339
A
HOH
120
3
HOH
HOH
340
A
HOH
121
3
HOH
HOH
341
A
HOH
122
3
HOH
HOH
342
A
HOH
123
3
HOH
HOH
343
A
HOH
124
3
HOH
HOH
344
A
HOH
125
3
HOH
HOH
345
A
HOH
126
3
HOH
HOH
346
A
HOH
127
3
HOH
HOH
347
A
HOH
128
3
HOH
HOH
348
A
HOH
129
3
HOH
HOH
349
A
HOH
130
3
HOH
HOH
350
A
HOH
131
3
HOH
HOH
351
A
HOH
132
3
HOH
HOH
352
A
HOH
133
3
HOH
HOH
353
A
HOH
134
3
HOH
HOH
354
A
HOH
135
3
HOH
HOH
355
A
HOH
136
3
HOH
HOH
356
A
HOH
137
3
HOH
HOH
357
A
HOH
138
3
HOH
HOH
358
A
HOH
139
3
HOH
HOH
359
A
HOH
140
3
HOH
HOH
360
A
HOH
141
3
HOH
HOH
361
A
HOH
142
3
HOH
HOH
362
A
HOH
143
3
HOH
HOH
363
A
HOH
144
3
HOH
HOH
364
A
HOH
145
3
HOH
HOH
365
A
HOH
146
3
HOH
HOH
366
A
HOH
147
3
HOH
HOH
367
A
HOH
148
3
HOH
HOH
368
A
HOH
149
3
HOH
HOH
369
A
HOH
150
3
HOH
HOH
370
A
HOH
151
3
HOH
HOH
371
A
HOH
152
3
HOH
HOH
372
A
HOH
153
3
HOH
HOH
373
A
HOH
154
3
HOH
HOH
374
A
HOH
155
3
HOH
HOH
375
A
HOH
156
3
HOH
HOH
376
A
HOH
157
3
HOH
HOH
377
A
HOH
158
3
HOH
HOH
378
A
HOH
159
3
HOH
HOH
379
A
HOH
160
3
HOH
HOH
380
A
HOH
161
3
HOH
HOH
381
A
HOH
162
3
HOH
HOH
382
A
HOH
163
3
HOH
HOH
383
A
HOH
164
3
HOH
HOH
384
A
HOH
165
3
HOH
HOH
385
A
HOH
166
3
HOH
HOH
386
A
HOH
167
3
HOH
HOH
387
A
HOH
168
3
HOH
HOH
388
A
HOH
169
3
HOH
HOH
389
A
HOH
170
3
HOH
HOH
390
A
HOH
171
3
HOH
HOH
391
A
HOH
172
3
HOH
HOH
392
A
HOH
173
3
HOH
HOH
393
A
HOH
174
3
HOH
HOH
394
A
HOH
175
3
HOH
HOH
395
A
HOH
176
3
HOH
HOH
396
A
HOH
177
3
HOH
HOH
397
A
HOH
178
3
HOH
HOH
398
A
HOH
179
3
HOH
HOH
399
A
HOH
180
3
HOH
HOH
400
A
HOH
181
3
HOH
HOH
401
A
HOH
182
3
HOH
HOH
402
A
HOH
183
3
HOH
HOH
403
A
HOH
184
3
HOH
HOH
404
A
HOH
185
3
HOH
HOH
405
A
HOH
186
3
HOH
HOH
406
A
HOH
187
3
HOH
HOH
407
A
HOH
188
3
HOH
HOH
408
A
HOH
189
3
HOH
HOH
409
A
HOH
190
3
HOH
HOH
410
A
HOH
191
3
HOH
HOH
411
A
HOH
192
3
HOH
HOH
412
A
HOH
193
3
HOH
HOH
413
A
HOH
194
3
HOH
HOH
414
A
n
1
-11
A
n
2
-10
A
SER
-9
n
3
SER
-9
A
ASP
-8
n
4
ASP
-8
A
LYS
-7
n
5
LYS
-7
A
ILE
-6
n
6
ILE
-6
A
HIS
-5
n
7
HIS
-5
A
HIS
-4
n
8
HIS
-4
A
HIS
-3
n
9
HIS
-3
A
HIS
-2
n
10
HIS
-2
A
HIS
-1
n
11
HIS
-1
A
HIS
0
n
12
HIS
0
A
MSE
1
n
13
MSE
1
A
GLU
2
n
14
GLU
2
A
THR
3
n
15
THR
3
A
MSE
4
n
16
MSE
4
A
PHE
5
n
17
PHE
5
A
ASP
6
n
18
ASP
6
A
THR
7
n
19
THR
7
A
LEU
8
n
20
LEU
8
A
LEU
9
n
21
LEU
9
A
GLN
10
n
22
GLN
10
A
LEU
11
n
23
LEU
11
A
PRO
12
n
24
PRO
12
A
LEU
13
n
25
LEU
13
A
PHE
14
n
26
PHE
14
A
GLN
15
n
27
GLN
15
A
GLY
16
n
28
GLY
16
A
LEU
17
n
29
LEU
17
A
CYS
18
n
30
CYS
18
A
HIS
19
n
31
HIS
19
A
GLU
20
n
32
GLU
20
A
ASP
21
n
33
ASP
21
A
PHE
22
n
34
PHE
22
A
THR
23
n
35
THR
23
A
SER
24
n
36
SER
24
A
ILE
25
n
37
ILE
25
A
LEU
26
n
38
LEU
26
A
ASP
27
n
39
ASP
27
A
LYS
28
n
40
LYS
28
A
VAL
29
n
41
VAL
29
A
LYS
30
n
42
LYS
30
A
LEU
31
n
43
LEU
31
A
HIS
32
n
44
HIS
32
A
PHE
33
n
45
PHE
33
A
ILE
34
n
46
ILE
34
A
LYS
35
n
47
LYS
35
A
HIS
36
n
48
HIS
36
A
LYS
37
n
49
LYS
37
A
ALA
38
n
50
ALA
38
A
GLY
39
n
51
GLY
39
A
GLU
40
n
52
GLU
40
A
THR
41
n
53
THR
41
A
ILE
42
n
54
ILE
42
A
ILE
43
n
55
ILE
43
A
LYS
44
n
56
LYS
44
A
SER
45
n
57
SER
45
A
GLY
46
n
58
GLY
46
A
ASN
47
n
59
ASN
47
A
PRO
48
n
60
PRO
48
A
CYS
49
n
61
CYS
49
A
THR
50
n
62
THR
50
A
GLN
51
n
63
GLN
51
A
LEU
52
n
64
LEU
52
A
CYS
53
n
65
CYS
53
A
PHE
54
n
66
PHE
54
A
LEU
55
n
67
LEU
55
A
LEU
56
n
68
LEU
56
A
LYS
57
n
69
LYS
57
A
GLY
58
n
70
GLY
58
A
GLU
59
n
71
GLU
59
A
ILE
60
n
72
ILE
60
A
SER
61
n
73
SER
61
A
ILE
62
n
74
ILE
62
A
VAL
63
n
75
VAL
63
A
THR
64
n
76
THR
64
A
ASN
65
n
77
ASN
65
A
ALA
66
n
78
ALA
66
A
LYS
67
n
79
LYS
67
A
GLU
68
n
80
GLU
68
A
ASN
69
n
81
ASN
69
A
ILE
70
n
82
ILE
70
A
TYR
71
n
83
TYR
71
A
THR
72
n
84
THR
72
A
VAL
73
n
85
VAL
73
A
ILE
74
n
86
ILE
74
A
GLU
75
n
87
GLU
75
A
GLN
76
n
88
GLN
76
A
ILE
77
n
89
ILE
77
A
GLU
78
n
90
GLU
78
A
ALA
79
n
91
ALA
79
A
PRO
80
n
92
PRO
80
A
TYR
81
n
93
TYR
81
A
LEU
82
n
94
LEU
82
A
ILE
83
n
95
ILE
83
A
GLU
84
n
96
GLU
84
A
PRO
85
n
97
PRO
85
A
GLN
86
n
98
GLN
86
A
SER
87
n
99
SER
87
A
LEU
88
n
100
LEU
88
A
PHE
89
n
101
PHE
89
A
GLY
90
n
102
GLY
90
A
MSE
91
n
103
MSE
91
A
ASN
92
n
104
ASN
92
A
THR
93
n
105
THR
93
A
ASN
94
n
106
ASN
94
A
TYR
95
n
107
TYR
95
A
ALA
96
n
108
ALA
96
A
SER
97
n
109
SER
97
A
SER
98
n
110
SER
98
A
TYR
99
n
111
TYR
99
A
VAL
100
n
112
VAL
100
A
ALA
101
n
113
ALA
101
A
HIS
102
n
114
HIS
102
A
THR
103
n
115
THR
103
A
GLU
104
n
116
GLU
104
A
VAL
105
n
117
VAL
105
A
HIS
106
n
118
HIS
106
A
THR
107
n
119
THR
107
A
VAL
108
n
120
VAL
108
A
CYS
109
n
121
CYS
109
A
ILE
110
n
122
ILE
110
A
SER
111
n
123
SER
111
A
LYS
112
n
124
LYS
112
A
ALA
113
n
125
ALA
113
A
PHE
114
n
126
PHE
114
A
VAL
115
n
127
VAL
115
A
LEU
116
n
128
LEU
116
A
SER
117
n
129
SER
117
A
ASP
118
n
130
ASP
118
A
LEU
119
n
131
LEU
119
A
PHE
120
n
132
PHE
120
A
ARG
121
n
133
ARG
121
A
TYR
122
n
134
TYR
122
A
ASP
123
n
135
ASP
123
A
ILE
124
n
136
ILE
124
A
PHE
125
n
137
PHE
125
A
ARG
126
n
138
ARG
126
A
LEU
127
n
139
LEU
127
A
ASN
128
n
140
ASN
128
A
TYR
129
n
141
TYR
129
A
MSE
130
n
142
MSE
130
A
ASN
131
n
143
ASN
131
A
ILE
132
n
144
ILE
132
A
VAL
133
n
145
VAL
133
A
SER
134
n
146
SER
134
A
ASN
135
n
147
ASN
135
A
ARG
136
n
148
ARG
136
A
ALA
137
n
149
ALA
137
A
GLN
138
n
150
GLN
138
A
ASN
139
n
151
ASN
139
A
LEU
140
n
152
LEU
140
A
TYR
141
n
153
TYR
141
A
SER
142
n
154
SER
142
A
ARG
143
n
155
ARG
143
A
LEU
144
n
156
LEU
144
A
TRP
145
n
157
TRP
145
A
ASP
146
n
158
ASP
146
A
GLU
147
n
159
GLU
147
A
PRO
148
n
160
PRO
148
A
THR
149
n
161
THR
149
A
LEU
150
n
162
LEU
150
A
ASP
151
n
163
ASP
151
A
LEU
152
n
164
LEU
152
A
LYS
153
n
165
LYS
153
A
SER
154
n
166
SER
154
A
LYS
155
n
167
LYS
155
A
ILE
156
n
168
ILE
156
A
ILE
157
n
169
ILE
157
A
ARG
158
n
170
ARG
158
A
PHE
159
n
171
PHE
159
A
PHE
160
n
172
PHE
160
A
LEU
161
n
173
LEU
161
A
SER
162
n
174
SER
162
A
HIS
163
n
175
HIS
163
A
CYS
164
n
176
CYS
164
A
GLU
165
n
177
GLU
165
A
LYS
166
n
178
LYS
166
A
PRO
167
n
179
PRO
167
A
GLN
168
n
180
GLN
168
A
GLY
169
n
181
GLY
169
A
GLU
170
n
182
GLU
170
A
LYS
171
n
183
LYS
171
A
THR
172
n
184
THR
172
A
PHE
173
n
185
PHE
173
A
LYS
174
n
186
LYS
174
A
VAL
175
n
187
VAL
175
A
LYS
176
n
188
LYS
176
A
MSE
177
n
189
MSE
177
A
ASP
178
n
190
ASP
178
A
ASP
179
n
191
ASP
179
A
LEU
180
n
192
LEU
180
A
ALA
181
n
193
ALA
181
A
ARG
182
n
194
ARG
182
A
CYS
183
n
195
CYS
183
A
LEU
184
n
196
LEU
184
A
ASP
185
n
197
ASP
185
A
ASP
186
n
198
ASP
186
A
THR
187
n
199
THR
187
A
ARG
188
n
200
ARG
188
A
LEU
189
n
201
LEU
189
A
ASN
190
n
202
ASN
190
A
ILE
191
n
203
ILE
191
A
SER
192
n
204
SER
192
A
LYS
193
n
205
LYS
193
A
THR
194
n
206
THR
194
A
LEU
195
n
207
LEU
195
A
ASN
196
n
208
ASN
196
A
GLU
197
n
209
GLU
197
A
LEU
198
n
210
LEU
198
A
GLN
199
n
211
GLN
199
A
ASP
200
n
212
ASP
200
A
ASN
201
n
213
ASN
201
A
GLY
202
n
214
GLY
202
A
LEU
203
n
215
LEU
203
A
ILE
204
n
216
ILE
204
A
GLU
205
n
217
GLU
205
A
LEU
206
n
218
LEU
206
A
HIS
207
n
219
HIS
207
A
ARG
208
n
220
ARG
208
A
LYS
209
n
221
LYS
209
A
GLU
210
n
222
GLU
210
A
ILE
211
n
223
ILE
211
A
LEU
212
n
224
LEU
212
A
ILE
213
n
225
ILE
213
A
PRO
214
n
226
PRO
214
A
ASP
215
n
227
ASP
215
A
ALA
216
n
228
ALA
216
A
GLN
217
n
229
GLN
217
A
LYS
218
n
230
LYS
218
A
LEU
219
n
231
LEU
219
A
LEU
220
n
232
LEU
220
A
1.3136
0.9782
-0.5254
1.6663
-0.1776
0.2588
-0.0555
-0.2061
-0.0828
0.1045
0.0442
0.0182
-0.0197
0.1377
0.0114
-0.1211
-0.0239
-0.0332
0.0545
0.1586
-0.0891
refined
-23.4662
43.9930
1.7133
X-RAY DIFFRACTION
A
-9
A
3
A
220
A
232
X-RAY DIFFRACTION
1
author_and_software_defined_assembly
PISA,PQS
2
dimeric
7830
-42
22000
A
MSE
1
SELENOMETHIONINE
A
MSE
13
MET
A
MSE
4
SELENOMETHIONINE
A
MSE
16
MET
A
MSE
91
SELENOMETHIONINE
A
MSE
103
MET
A
MSE
130
SELENOMETHIONINE
A
MSE
142
MET
A
MSE
177
SELENOMETHIONINE
A
MSE
189
MET
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
0.5000000000
0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
12_564
x,x-y+1,-z-1/6
crystal symmetry operation
-57.9900000000
100.4416263309
-19.9398333333
A
N
HIS
36
A
N
HIS
48
A
O
VAL
105
A
O
VAL
117
A
O
ILE
110
A
O
ILE
122
A
N
LEU
52
A
N
LEU
64
A
N
LEU
55
A
N
LEU
67
A
O
TYR
81
A
O
TYR
93
A
N
ILE
43
A
N
ILE
55
A
O
TYR
99
A
O
TYR
111
A
O
SER
98
A
O
SER
110
A
N
VAL
63
A
N
VAL
75
A
N
ILE
62
A
N
ILE
74
A
O
GLU
75
A
O
GLU
87
A
N
THR
72
A
N
THR
84
A
O
LYS
174
A
O
LYS
186
A
N
LYS
171
A
N
LYS
183
A
O
ILE
213
A
O
ILE
225
A
O
GLU
210
A
O
GLU
222
A
N
HIS
207
A
N
HIS
219
1
A
HOH
339
I
HOH
1
A
OG
SER
-9
A
OG
SER
3
1
Y
1
A
CE
LYS
28
A
CE
LYS
40
1
Y
1
A
NZ
LYS
28
A
NZ
LYS
40
1
Y
1
A
CD
LYS
67
A
CD
LYS
79
1
Y
1
A
CE
LYS
67
A
CE
LYS
79
1
Y
1
A
NZ
LYS
67
A
NZ
LYS
79
1
Y
1
A
CG
ARG
208
A
CG
ARG
220
1
Y
1
A
CD
ARG
208
A
CD
ARG
220
1
Y
1
A
NE
ARG
208
A
NE
ARG
220
1
Y
1
A
CZ
ARG
208
A
CZ
ARG
220
1
Y
1
A
NH1
ARG
208
A
NH1
ARG
220
1
Y
1
A
NH2
ARG
208
A
NH2
ARG
220
1
Y
1
A
CD
LYS
218
A
CD
LYS
230
1
Y
1
A
CE
LYS
218
A
CE
LYS
230
1
Y
1
A
NZ
LYS
218
A
NZ
LYS
230
1
Y
1
A
MSE
-11
A
MSE
1
1
Y
1
A
GLY
-10
A
GLY
2
1
Y
1
A
THR
7
-129.31
-82.61
1
A
GLU
84
38.44
60.79
1
A
ASP
118
-107.65
-66.62
1
A
PRO
167
-90.13
46.48
38.566
-1.330
-0.660
0.000
-1.330
0.000
1.990
0.960
0.939
1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. THERE EXISTS A PARTIAL DISULFIDE BOND BETWEEN CYS 53 AND CYS 109.
0.228
0.177
0.18
2.150
29.2
1332
25047
5.000
99.870
8.237
0.111
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
MAD
0.140
0.146
0.800
0.800
1.200
MAXIMUM LIKELIHOOD WITH PHASES
BABINET MODEL WITH MASK
2.150
29.2
187
2092
42
0
1863
0.016
0.022
2000
0.001
0.020
1825
1.406
1.966
2700
0.781
3.000
4272
5.560
5.000
229
35.444
24.796
98
12.987
15.000
369
15.613
15.000
8
0.084
0.200
312
0.006
0.020
2116
0.001
0.020
379
0.210
0.200
377
0.173
0.200
1741
0.181
0.200
945
0.085
0.200
1223
0.143
0.200
142
0.179
0.200
20
0.240
0.200
103
0.232
0.200
15
2.395
3.000
1262
0.529
3.000
462
3.226
5.000
1914
5.604
8.000
897
7.474
11.000
786
0.295
0.229
2.206
97
1808
20
100.000
2.10
29.91
1ZYB
28282
0.088
0.088
1
6.400
6.800
99.900
0.766
2.10
2.15
1.000
2027
0.766
1
4.200
98.800
0.649
2.15
2.21
1.200
1986
0.649
1
5.000
100.000
0.617
2.21
2.28
1.200
1951
0.617
1
6.300
100.000
0.517
2.28
2.35
1.500
1904
0.517
1
7.400
100.000
0.404
2.35
2.42
1.900
1823
0.404
1
7.300
100.000
0.315
2.42
2.51
2.400
1797
0.315
1
7.300
100.000
0.263
2.51
2.60
2.900
1724
0.263
1
7.300
100.000
0.204
2.60
2.71
3.700
1642
0.204
1
7.300
100.000
0.162
2.71
2.83
4.700
1603
0.162
1
7.300
100.000
0.123
2.83
2.97
6.100
1531
0.123
1
7.300
100.000
0.099
2.97
3.13
7.200
1467
0.099
1
7.200
100.000
0.085
3.13
3.32
7.900
1380
0.085
1
7.200
100.000
0.073
3.32
3.55
8.900
1311
0.073
1
7.200
100.000
0.064
3.55
3.83
9.400
1220
0.064
1
7.100
100.000
0.058
3.83
4.20
10.600
1133
0.058
1
7.100
100.000
0.052
4.20
4.70
11.200
1038
0.052
1
7.000
100.000
0.049
4.70
5.42
12.200
936
0.049
1
6.900
100.000
0.052
5.42
6.64
10.300
797
0.052
1
6.800
100.000
0.037
6.64
9.39
14.400
637
0.037
1
6.400
99.800
0.032
9.39
29.91
16.300
375
0.032
1
5.600
96.000
refinement
Murshudov, G.N.
ccp4@dl.ac.uk
Fortran
http://www.ccp4.ac.uk/main.html
REFMAC
5.2.0005
data scaling
Phil Evans
pre@mrc-lmb.cam.ac.uk
Fortran
http://www.ccp4.ac.uk/dist/html/INDEX.html
SCALA
data extraction
PDB
sw-help@rcsb.rutgers.edu
Jan. 30, 2005
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
1.601
data reduction
MOSFLM
data scaling
CCP4
(SCALA)
phasing
SOLVE
Crystal structure of transcription regulator from Bacteroides thetaiotaomicron VPI-5482 at 2.15 A resolution
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
A
HIS
-4
A
HIS
8
HELX_P
A
ASP
6
A
ASP
18
1
1
11
A
THR
7
A
THR
19
HELX_P
A
GLN
15
A
GLN
27
5
2
9
A
CYS
18
A
CYS
30
HELX_P
A
LYS
28
A
LYS
40
1
3
11
A
LYS
67
A
LYS
79
HELX_P
A
ILE
70
A
ILE
82
5
4
4
A
GLU
84
A
GLU
96
HELX_P
A
PHE
89
A
PHE
101
5
5
6
A
LYS
112
A
LYS
124
HELX_P
A
ASP
118
A
ASP
130
1
6
7
A
LEU
119
A
LEU
131
HELX_P
A
ARG
121
A
ARG
133
5
7
3
A
TYR
122
A
TYR
134
HELX_P
A
LEU
144
A
LEU
156
1
8
23
A
ASP
151
A
ASP
163
HELX_P
A
SER
162
A
SER
174
1
9
12
A
LYS
176
A
LYS
188
HELX_P
A
ASP
185
A
ASP
197
1
10
10
A
THR
187
A
THR
199
HELX_P
A
ASN
201
A
ASN
213
1
11
15
A
ASP
215
A
ASP
227
HELX_P
A
LEU
220
A
LEU
232
5
12
6
disulf
2.055
B
B
A
CYS
53
A
SG
CYS
65
1_555
A
CYS
109
A
SG
CYS
121
1_555
covale
1.324
both
A
HIS
0
A
C
HIS
12
1_555
A
MSE
1
A
N
MSE
13
1_555
covale
1.326
both
A
MSE
1
A
C
MSE
13
1_555
A
GLU
2
A
N
GLU
14
1_555
covale
1.328
both
A
THR
3
A
C
THR
15
1_555
A
MSE
4
A
N
MSE
16
1_555
covale
1.321
both
A
MSE
4
A
C
MSE
16
1_555
A
PHE
5
A
N
PHE
17
1_555
covale
1.332
both
A
GLY
90
A
C
GLY
102
1_555
A
MSE
91
A
N
MSE
103
1_555
covale
1.332
both
A
MSE
91
A
C
MSE
103
1_555
A
ASN
92
A
N
ASN
104
1_555
covale
1.331
both
A
TYR
129
A
C
TYR
141
1_555
A
MSE
130
A
N
MSE
142
1_555
covale
1.322
both
A
MSE
130
A
C
MSE
142
1_555
A
ASN
131
A
N
ASN
143
1_555
covale
1.307
both
A
LYS
176
A
C
LYS
188
1_555
A
MSE
177
A
N
MSE
189
1_555
covale
1.332
both
A
MSE
177
A
C
MSE
189
1_555
A
ASP
178
A
N
ASP
190
1_555
TRANSCRIPTION REGULATOR
np_813211.1, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, TRANSCRIPTION REGULATOR
A
ALA
79
A
ALA
91
1
A
PRO
80
A
PRO
92
-5.17
NP_813211
GB
1
1
29349708
METMFDTLLQLPLFQGLCHEDFTSILDKVKLHFIKHKAGETIIKSGNPCTQLCFLLKGEISIVTNAKENIYTVIEQIEAP
YLIEPQSLFGMNTNYASSYVAHTEVHTVCISKAFVLSDLFRYDIFRLNYMNIVSNRAQNLYSRLWDEPTLDLKSKIIRFF
LSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNELQDNGLIELHRKEILIPDAQKLL
1
220
1ZYB
1
220
29349708
A
1
13
232
1
expression tag
MSE
-11
1ZYB
A
29349708
GB
1
1
expression tag
GLY
-10
1ZYB
A
29349708
GB
2
1
expression tag
SER
-9
1ZYB
A
29349708
GB
3
1
expression tag
ASP
-8
1ZYB
A
29349708
GB
4
1
expression tag
LYS
-7
1ZYB
A
29349708
GB
5
1
expression tag
ILE
-6
1ZYB
A
29349708
GB
6
1
expression tag
HIS
-5
1ZYB
A
29349708
GB
7
1
expression tag
HIS
-4
1ZYB
A
29349708
GB
8
1
expression tag
HIS
-3
1ZYB
A
29349708
GB
9
1
expression tag
HIS
-2
1ZYB
A
29349708
GB
10
1
expression tag
HIS
-1
1ZYB
A
29349708
GB
11
1
expression tag
HIS
0
1ZYB
A
29349708
GB
12
1
MET
modified residue
MSE
1
1ZYB
A
29349708
GB
1
13
1
MET
modified residue
MSE
4
1ZYB
A
29349708
GB
4
16
1
MET
modified residue
MSE
91
1ZYB
A
29349708
GB
91
103
1
MET
modified residue
MSE
130
1ZYB
A
29349708
GB
130
142
1
MET
modified residue
MSE
177
1ZYB
A
29349708
GB
177
189
4
7
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
HIS
32
A
HIS
44
A
HIS
36
A
HIS
48
A
VAL
105
A
VAL
117
A
SER
111
A
SER
123
A
GLN
51
A
GLN
63
A
LYS
57
A
LYS
69
A
TYR
81
A
TYR
93
A
ILE
83
A
ILE
95
A
THR
41
A
THR
53
A
ILE
43
A
ILE
55
A
SER
98
A
SER
110
A
ALA
101
A
ALA
113
A
GLU
59
A
GLU
71
A
ASN
65
A
ASN
77
A
THR
72
A
THR
84
A
GLU
78
A
GLU
90
A
LYS
171
A
LYS
183
A
LYS
174
A
LYS
186
A
GLU
210
A
GLU
222
A
ILE
213
A
ILE
225
A
GLU
205
A
GLU
217
A
HIS
207
A
HIS
219
BINDING SITE FOR RESIDUE GOL A 221
A
GOL
221
Software
5
BINDING SITE FOR RESIDUE GOL A 222
A
GOL
222
Software
4
BINDING SITE FOR RESIDUE GOL A 223
A
GOL
223
Software
5
BINDING SITE FOR RESIDUE GOL A 224
A
GOL
224
Software
5
BINDING SITE FOR RESIDUE GOL A 225
A
GOL
225
Software
6
BINDING SITE FOR RESIDUE GOL A 226
A
GOL
226
Software
8
BINDING SITE FOR RESIDUE GOL A 227
A
GOL
227
Software
9
A
THR
64
A
THR
76
5
1_555
A
ASN
65
A
ASN
77
5
1_555
A
ALA
96
A
ALA
108
5
1_555
A
TRP
145
A
TRP
157
5
12_564
A
HOH
237
I
HOH
5
1_555
A
HIS
36
A
HIS
48
4
1_555
A
ILE
42
A
ILE
54
4
1_555
A
ILE
43
A
ILE
55
4
1_555
A
GLN
51
A
GLN
63
4
1_555
A
HIS
-2
A
HIS
10
5
1_555
A
MSE
1
A
MSE
13
5
1_555
A
GLU
2
A
GLU
14
5
1_555
A
PHE
5
A
PHE
17
5
1_555
A
HOH
379
I
HOH
5
1_555
A
HIS
-1
A
HIS
11
5
10_555
A
LYS
-7
A
LYS
5
5
1_555
A
HIS
0
A
HIS
12
5
10_555
A
THR
3
A
THR
15
5
10_555
A
HOH
388
I
HOH
5
1_555
A
VAL
175
A
VAL
187
6
1_555
A
MSE
177
A
MSE
189
6
1_555
A
HIS
207
A
HIS
219
6
1_555
A
LYS
209
A
LYS
221
6
1_555
A
GLU
210
A
GLU
222
6
1_555
A
HOH
311
I
HOH
6
1_555
A
PHE
114
A
PHE
126
8
5_555
A
SER
117
A
SER
129
8
5_555
A
ASP
118
A
ASP
130
8
5_555
A
LEU
206
A
LEU
218
8
1_555
A
HIS
207
A
HIS
219
8
1_555
A
HOH
326
I
HOH
8
1_555
A
HOH
372
I
HOH
8
1_555
A
HOH
381
I
HOH
8
1_555
A
ARG
136
A
ARG
148
9
1_555
A
ASN
139
A
ASN
151
9
1_555
A
LEU
140
A
LEU
152
9
1_555
A
TYR
141
A
TYR
153
9
12_564
A
ARG
143
A
ARG
155
9
1_555
A
SER
162
A
SER
174
9
1_555
A
CYS
164
A
CYS
176
9
1_555
A
GLU
165
A
GLU
177
9
1_555
A
HOH
354
I
HOH
9
1_555
179
P 65 2 2