0.014214
0.008207
0.000000
0.000000
0.016413
0.000000
0.000000
0.000000
0.009358
0.00000
0.00000
0.00000
Giardina, G.
Cutruzzola, F.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
70.351
70.351
106.866
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
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
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 H10 O
74.122
TERTIARY-BUTYL ALCOHOL
2-METHYL-2-PROPANOL
non-polymer
C4 H9 N O3
119.119
y
THREONINE
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
C
N
124
N
O
N
125
N
C
N
126
N
O
N
127
N
C
N
128
N
O
N
129
N
H
N
130
N
H
N
131
N
H
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
N
N
159
S
C
N
160
N
C
N
161
N
O
N
162
S
C
N
163
N
C
N
164
N
C
N
165
N
C
N
166
N
O
N
167
N
H
N
168
N
H
N
169
N
H
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
N
N
181
S
C
N
182
N
C
N
183
N
O
N
184
N
C
N
185
N
C
N
186
N
C
N
187
N
C
N
188
N
O
N
189
N
H
N
190
N
H
N
191
N
H
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
N
N
203
S
C
N
204
N
C
N
205
N
O
N
206
N
C
N
207
N
C
N
208
N
C
N
209
N
C
N
210
N
N
N
211
N
O
N
212
N
H
N
213
N
H
N
214
N
H
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
N
N
228
S
C
N
229
N
C
N
230
N
O
N
231
N
C
N
232
N
C
N
233
N
S
N
234
N
C
N
235
N
O
N
236
N
H
N
237
N
H
N
238
N
H
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
N
N
248
S
C
N
249
N
C
N
250
N
O
N
251
N
C
Y
252
N
C
Y
253
N
C
Y
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
N
258
N
O
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
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
N
N
271
S
C
N
272
N
C
N
273
N
O
N
274
N
C
N
275
N
C
N
276
N
C
N
277
N
O
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
N
N
288
S
C
N
289
N
C
N
290
N
O
N
291
N
C
N
292
N
O
N
293
N
O
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
O
N
302
N
C
N
303
N
C
N
304
N
C
N
305
N
C
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
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
N
N
317
S
C
N
318
N
C
N
319
N
O
N
320
R
C
N
321
N
O
N
322
N
C
N
323
N
O
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
N
N
334
S
C
N
335
N
C
N
336
N
O
N
337
N
C
Y
338
N
C
Y
339
N
C
Y
340
N
C
Y
341
N
C
Y
342
N
C
Y
343
N
C
N
344
N
O
N
345
N
O
N
346
N
H
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
N
N
358
S
C
N
359
N
C
N
360
N
O
N
361
N
C
N
362
N
C
N
363
N
C
N
364
N
O
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
H
N
374
N
H
N
375
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
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
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
doub
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
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
doub
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
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
doub
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
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
doub
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
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
doub
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
Y
246
N
doub
Y
247
N
sing
Y
248
N
sing
N
249
N
sing
Y
250
N
doub
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
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
doub
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
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
doub
N
282
N
sing
N
283
N
sing
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
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
doub
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
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
doub
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
Y
329
N
doub
Y
330
N
sing
Y
331
N
sing
N
332
N
sing
Y
333
N
doub
N
334
N
sing
Y
335
N
doub
N
336
N
sing
Y
337
N
sing
N
338
N
sing
N
339
N
sing
N
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
doub
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
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
US
Plos One
1932-6203
8
e81324
e81324
10.1371/journal.pone.0081324
24278422
Investigating the Allosteric Regulation of YfiN from Pseudomonas aeruginosa: Clues from the Structure of the Catalytic Domain.
2013
10.2210/pdb4iob/pdb
pdb_00004iob
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
2012-05-18
ADSC QUANTUM 210
Diamond (111), Ge(220)
SINGLE WAVELENGTH
M
x-ray
1
0.933
1.0
ID14-1
ESRF
0.933
SYNCHROTRON
ESRF BEAMLINE ID14-1
17540.955
Diguanylate cyclase TpbB
2.7.7.65
Diguanylate cyclase (GGDEF) domain, UNP residues 254-414
1
man
polymer
74.122
TERTIARY-BUTYL ALCOHOL
1
syn
non-polymer
92.094
GLYCEROL
1
syn
non-polymer
no
no
LTSLPNRAFFEGRLSRALRDANEHREQLAVLFIDSDRFKEINDRLGHAAGDTVLVNIAMRIRGQLRESDLVARLGGDEFA
VLLAPLASGADALRIADNIIASMQAPIRLSDGSTVSTSLTIGIALYPEHADTPAALLHDADMAMYIAKRQARGSRRLAEL
N
LTSLPNRAFFEGRLSRALRDANEHREQLAVLFIDSDRFKEINDRLGHAAGDTVLVNIAMRIRGQLRESDLVARLGGDEFA
VLLAPLASGADALRIADNIIASMQAPIRLSDGSTVSTSLTIGIALYPEHADTPAALLHDADMAMYIAKRQARGSRRLAEL
N
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
PAO1
sample
PA1120, tpbB
208964
Pseudomonas aeruginosa
469008
Escherichia coli
BL21(DE3)
plasmid
pET24b
1
2.18
43.48
VAPOR DIFFUSION, SITTING DROP
5.6
300nl+300nl of 3.7 mg/ml protein solution (100 mM NaCl, 10 mM Tris pH=8.0, 2% glycerol) and 0.1 M Sodium Citrate dehydrate pH 5.6, 35% v/v tert-butanol., VAPOR DIFFUSION, SITTING DROP, temperature 294K
294
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_site
repository
Initial release
Database references
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
2013-12-04
1
1
2014-01-08
1
2
2017-11-15
1
3
2023-09-20
_software.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2013-01-07
REL
REL
TBU
TERTIARY-BUTYL ALCOHOL
GOL
GLYCEROL
2WB4
PDB ENTRY 2WB4
PDB
experimental model
TBU
1
2
TBU
TBU
501
A
GOL
1
3
GOL
GOL
502
A
LEU
254
n
1
LEU
254
A
THR
255
n
2
THR
255
A
SER
256
n
3
SER
256
A
LEU
257
n
4
LEU
257
A
PRO
258
n
5
PRO
258
A
ASN
259
n
6
ASN
259
A
ARG
260
n
7
ARG
260
A
ALA
261
n
8
ALA
261
A
PHE
262
n
9
PHE
262
A
PHE
263
n
10
PHE
263
A
GLU
264
n
11
GLU
264
A
GLY
265
n
12
GLY
265
A
ARG
266
n
13
ARG
266
A
LEU
267
n
14
LEU
267
A
SER
268
n
15
SER
268
A
ARG
269
n
16
ARG
269
A
ALA
270
n
17
ALA
270
A
LEU
271
n
18
LEU
271
A
ARG
272
n
19
ARG
272
A
ASP
273
n
20
ASP
273
A
ALA
274
n
21
ALA
274
A
ASN
275
n
22
ASN
275
A
GLU
276
n
23
GLU
276
A
HIS
277
n
24
HIS
277
A
ARG
278
n
25
ARG
278
A
GLU
279
n
26
GLU
279
A
GLN
280
n
27
GLN
280
A
LEU
281
n
28
LEU
281
A
ALA
282
n
29
ALA
282
A
VAL
283
n
30
VAL
283
A
LEU
284
n
31
LEU
284
A
PHE
285
n
32
PHE
285
A
ILE
286
n
33
ILE
286
A
ASP
287
n
34
ASP
287
A
SER
288
n
35
SER
288
A
ASP
289
n
36
ASP
289
A
ARG
290
n
37
ARG
290
A
PHE
291
n
38
PHE
291
A
LYS
292
n
39
LYS
292
A
GLU
293
n
40
GLU
293
A
ILE
294
n
41
ILE
294
A
ASN
295
n
42
ASN
295
A
ASP
296
n
43
ASP
296
A
ARG
297
n
44
ARG
297
A
LEU
298
n
45
LEU
298
A
GLY
299
n
46
GLY
299
A
HIS
300
n
47
HIS
300
A
ALA
301
n
48
ALA
301
A
ALA
302
n
49
ALA
302
A
GLY
303
n
50
GLY
303
A
ASP
304
n
51
ASP
304
A
THR
305
n
52
THR
305
A
VAL
306
n
53
VAL
306
A
LEU
307
n
54
LEU
307
A
VAL
308
n
55
VAL
308
A
ASN
309
n
56
ASN
309
A
ILE
310
n
57
ILE
310
A
ALA
311
n
58
ALA
311
A
MET
312
n
59
MET
312
A
ARG
313
n
60
ARG
313
A
ILE
314
n
61
ILE
314
A
ARG
315
n
62
ARG
315
A
GLY
316
n
63
GLY
316
A
GLN
317
n
64
GLN
317
A
LEU
318
n
65
LEU
318
A
ARG
319
n
66
ARG
319
A
GLU
320
n
67
GLU
320
A
SER
321
n
68
SER
321
A
ASP
322
n
69
ASP
322
A
LEU
323
n
70
LEU
323
A
VAL
324
n
71
VAL
324
A
ALA
325
n
72
ALA
325
A
ARG
326
n
73
ARG
326
A
LEU
327
n
74
LEU
327
A
GLY
328
n
75
GLY
328
A
GLY
329
n
76
GLY
329
A
ASP
330
n
77
ASP
330
A
GLU
331
n
78
GLU
331
A
PHE
332
n
79
PHE
332
A
ALA
333
n
80
ALA
333
A
VAL
334
n
81
VAL
334
A
LEU
335
n
82
LEU
335
A
LEU
336
n
83
LEU
336
A
ALA
337
n
84
ALA
337
A
PRO
338
n
85
PRO
338
A
LEU
339
n
86
LEU
339
A
ALA
340
n
87
ALA
340
A
SER
341
n
88
SER
341
A
GLY
342
n
89
GLY
342
A
ALA
343
n
90
ALA
343
A
ASP
344
n
91
ASP
344
A
ALA
345
n
92
ALA
345
A
LEU
346
n
93
LEU
346
A
ARG
347
n
94
ARG
347
A
ILE
348
n
95
ILE
348
A
ALA
349
n
96
ALA
349
A
ASP
350
n
97
ASP
350
A
ASN
351
n
98
ASN
351
A
ILE
352
n
99
ILE
352
A
ILE
353
n
100
ILE
353
A
ALA
354
n
101
ALA
354
A
SER
355
n
102
SER
355
A
MET
356
n
103
MET
356
A
GLN
357
n
104
GLN
357
A
ALA
358
n
105
ALA
358
A
PRO
359
n
106
PRO
359
A
ILE
360
n
107
ILE
360
A
ARG
361
n
108
ARG
361
A
LEU
362
n
109
LEU
362
A
SER
363
n
110
SER
363
A
ASP
364
n
111
ASP
364
A
GLY
365
n
112
GLY
365
A
SER
366
n
113
SER
366
A
THR
367
n
114
THR
367
A
VAL
368
n
115
VAL
368
A
SER
369
n
116
SER
369
A
THR
370
n
117
THR
370
A
SER
371
n
118
SER
371
A
LEU
372
n
119
LEU
372
A
THR
373
n
120
THR
373
A
ILE
374
n
121
ILE
374
A
GLY
375
n
122
GLY
375
A
ILE
376
n
123
ILE
376
A
ALA
377
n
124
ALA
377
A
LEU
378
n
125
LEU
378
A
TYR
379
n
126
TYR
379
A
PRO
380
n
127
PRO
380
A
GLU
381
n
128
GLU
381
A
HIS
382
n
129
HIS
382
A
ALA
383
n
130
ALA
383
A
ASP
384
n
131
ASP
384
A
THR
385
n
132
THR
385
A
PRO
386
n
133
PRO
386
A
ALA
387
n
134
ALA
387
A
ALA
388
n
135
ALA
388
A
LEU
389
n
136
LEU
389
A
LEU
390
n
137
LEU
390
A
HIS
391
n
138
HIS
391
A
ASP
392
n
139
ASP
392
A
ALA
393
n
140
ALA
393
A
ASP
394
n
141
ASP
394
A
MET
395
n
142
MET
395
A
ALA
396
n
143
ALA
396
A
MET
397
n
144
MET
397
A
TYR
398
n
145
TYR
398
A
ILE
399
n
146
ILE
399
A
ALA
400
n
147
ALA
400
A
LYS
401
n
148
LYS
401
A
ARG
402
n
149
ARG
402
A
GLN
403
n
150
GLN
403
A
ALA
404
n
151
ALA
404
A
ARG
405
n
152
ARG
405
A
GLY
406
n
153
GLY
406
A
SER
407
n
154
SER
407
A
ARG
408
n
155
ARG
408
A
ARG
409
n
156
ARG
409
A
LEU
410
n
157
LEU
410
A
ALA
411
n
158
ALA
411
A
GLU
412
n
159
GLU
412
A
LEU
413
n
160
LEU
413
A
ASN
414
n
161
ASN
414
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
ALA
325
A
N
ALA
72
A
O
ALA
333
A
O
ALA
80
A
O
LEU
339
A
O
LEU
86
A
N
GLN
280
A
N
GLN
27
A
N
ASP
287
A
N
ASP
34
A
O
THR
373
A
O
THR
120
A
N
ILE
376
A
N
ILE
123
A
O
ARG
409
A
O
ARG
156
A
N
ILE
360
A
N
ILE
107
A
O
VAL
368
A
O
VAL
115
1
A
A
O
O
ALA
HIS
274
277
1.92
1
A
A
O
O
ALA
ALA
400
404
1.97
1
A
A
CZ
CD2
PHE
LEU
263
335
2.15
1
A
A
OD2
OH
ASP
TYR
350
398
2.15
1_555
5_555
1
A
GLU
320
-49.58
-16.42
1
A
LEU
413
-39.27
123.49
48.086
-2.11
-1.06
0.00
-2.11
0.00
3.17
0.889
0.888
HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
0.27978
0.27833
0.27841
2.78
40
217
4095
5.0
99.70
16.717
0.335
RANDOM
1
Isotropic
MOLECULAR REPLACEMENT
0.436
0.80
0.80
1.20
PDB ENTRY 2WB4
MAXIMUM LIKELIHOOD
MASK
2.78
40
0
1241
11
0
1230
0.001
0.019
1260
0.460
1.981
1703
3.002
5.000
162
22.269
22.500
60
15.058
15.000
215
11.077
15.000
17
0.031
0.200
199
0.001
0.021
952
0.378
0.343
2.849
13
230
20
95.67
57.9
2.78
40
4IOB
4359
4343
3
3
0.095
0.083
1
31.11
13.7
99.6
0.607
2.78
2.94
3.3
666
0.685
1
9.77
data collection
MAR345
phasing
MOLREP
refinement
REFMAC
5.6.0117
data reduction
XDS
data scaling
XSCALE
Crystal structure of the GGDEF domain of PA1120 (YfiN or TpbB) from Pseudomonas aeruginosa at 2.7 Ang.
1
N
N
2
N
N
3
N
N
A
ASN
259
A
ASN
6
HELX_P
A
HIS
277
A
HIS
24
1
1
19
A
ARG
290
A
ARG
37
HELX_P
A
GLY
299
A
GLY
46
1
2
10
A
GLY
299
A
GLY
46
HELX_P
A
GLY
316
A
GLY
63
1
3
18
A
SER
341
A
SER
88
HELX_P
A
MET
356
A
MET
103
1
4
16
A
THR
385
A
THR
132
HELX_P
A
ALA
404
A
ALA
151
1
5
20
LYASE
TpbB, YfiN, ggdef, DGC, PF00990, Diguanylate cyclase, GTP, c-di-GMP, cGpGp, cytosolic portion of a membrane protein, LYASE
A
ALA
337
A
ALA
84
1
A
PRO
338
A
PRO
85
-1.06
A
TYR
379
A
TYR
126
1
A
PRO
380
A
PRO
127
1.95
Q9I4L5_PSEAE
UNP
1
254
Q9I4L5
LTSLPNRAFFEGRLSRALRDANEHREQLAVLFIDSDRFKEINDRLGHAAGDTVLVNIAMRIRGQLRESDLVARLGGDEFA
VLLAPLASGADALRIADNIIASMQAPIRLSDGSTVSTSLTIGIALYPEHADTPAALLHDADMAMYIAKRQARGSRRLAEL
N
254
414
4IOB
254
414
Q9I4L5
A
1
1
161
5
2
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
A
LEU
323
A
LEU
70
A
GLY
328
A
GLY
75
A
GLU
331
A
GLU
78
A
LEU
339
A
LEU
86
A
GLN
280
A
GLN
27
A
SER
288
A
SER
35
A
LEU
372
A
LEU
119
A
TYR
379
A
TYR
126
A
ARG
408
A
ARG
155
A
LEU
410
A
LEU
157
A
ILE
360
A
ILE
107
A
ARG
361
A
ARG
108
A
THR
367
A
THR
114
A
VAL
368
A
VAL
115
BINDING SITE FOR RESIDUE TBU A 501
A
TBU
501
Software
4
BINDING SITE FOR RESIDUE GOL A 502
A
GOL
502
Software
6
A
ARG
266
A
ARG
13
4
8_545
A
ARG
269
A
ARG
16
4
8_545
A
GLY
299
A
GLY
46
4
1_555
A
HIS
300
A
HIS
47
4
1_555
A
ARG
290
A
ARG
37
6
1_555
A
PHE
291
A
PHE
38
6
1_555
A
LYS
292
A
LYS
39
6
1_555
A
ASP
330
A
ASP
77
6
1_555
A
ARG
347
A
ARG
94
6
6_554
A
LYS
401
A
LYS
148
6
1_555
179
P 65 2 2