0.017504
0.000000
0.000000
0.000000
0.017200
0.000000
0.000000
0.000000
0.005923
0.00000
0.00000
0.00000
Park, S.
Meyer, M.
Jones, A.D.
Yennawar, H.P.
Yennawar, N.H.
Nixon, B.T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
57.129
58.139
168.824
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
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
O4 S -2
96.063
SULFATE ION
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
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
N
N
251
S
C
N
252
N
C
N
253
N
O
N
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
N
261
N
O
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
H
N
271
N
H
N
272
N
H
N
273
N
N
N
274
S
C
N
275
N
C
N
276
N
O
N
277
N
C
N
278
N
C
N
279
N
C
N
280
N
O
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
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
N
C
N
295
N
O
N
296
N
O
N
297
N
H
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
S
N
305
N
O
N
306
N
O
N
307
N
O
N
308
N
O
N
309
N
N
N
310
S
C
N
311
N
C
N
312
N
O
N
313
R
C
N
314
N
O
N
315
N
C
N
316
N
O
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
N
N
327
S
C
N
328
N
C
N
329
N
O
N
330
N
C
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
C
Y
335
N
C
Y
336
N
C
N
337
N
O
N
338
N
O
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
N
N
351
S
C
N
352
N
C
N
353
N
O
N
354
N
C
N
355
N
C
N
356
N
C
N
357
N
O
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
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
sing
N
157
N
sing
N
158
N
doub
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
doub
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
doub
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
doub
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
doub
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
doub
N
291
N
doub
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
doub
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
doub
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
Y
321
N
doub
Y
322
N
sing
Y
323
N
sing
N
324
N
sing
Y
325
N
doub
N
326
N
sing
Y
327
N
doub
N
328
N
sing
Y
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
doub
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
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
US
FASEB J.
FAJOEC
2074
0892-6638
16
1964
1966
12368235
Two-component signaling in the AAA + ATPase DctD: binding Mg2+ and BeF3- selects between alternate dimeric states of the receiver domain
2002
US
FASEB J.
FAJOEC
2074
0892-6638
15
1326
1328
A dimeric two-component receiver domain inhibits the sigma54-dependent ATPase in DctD
2001
10.2210/pdb1l5z/pdb
pdb_00001l5z
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
MSC Blue Confocal Optical System
IMAGE PLATE
2001-09-30
RIGAKU RAXIS IV++
MSC Blue Confocal Optical System
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU200
16821.326
C4-DICARBOXYLATE TRANSPORT TRANSCRIPTIONAL REGULATORY PROTEIN DCTD
RECEIVER DOMAIN, RESIDUES 2-143
E121K
1
man
polymer
96.063
SULFATE ION
1
syn
non-polymer
92.094
GLYCEROL
4
syn
non-polymer
18.015
water
144
nat
water
DctDNL
no
no
SAAPSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILALDPDLPMIL
VTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEKKRRLVMENRSLRRAAEAASEGLKLAAALEHHHHHH
SAAPSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILALDPDLPMIL
VTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEKKRRLVMENRSLRRAAEAASEGLKLAAALEHHHHHH
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
Sinorhizobium
Escherichia
sample
dctD
382
Sinorhizobium meliloti
562
Escherichia coli
BL21/De3/pLysS
plasmid
pT143E121K
1
4.17
70.47
VAPOR DIFFUSION, HANGING DROP
7.5
HEPES, lithium sulfate, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
database_2
struct_conn
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Derived calculations
Version format compliance
Database references
Derived calculations
Data collection
Refinement description
1
0
2002-10-23
1
1
2008-04-28
1
2
2011-07-13
1
3
2021-10-27
1
4
2023-08-16
_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
CRYSTAL STRUCTURE OF THE RECEIVER DOMAIN AND LINKER REGION OF DCTD FROM SINORHIZOBIUM MELILOTI
CRYSTAL STRUCTURE OF MG2+ / BEF3- BOUND RECEIVER DOMAIN OF SINORHIZOBIUM MELILOTI DCTD
RCSB
Y
RCSB
2002-03-08
REL
REL
SO4
SULFATE ION
GOL
GLYCEROL
HOH
water
1QKK
PDB ENTRY 1QKK
PDB
experimental model
SO4
1
2
SO4
SO4
201
A
CRY
501
3
GOL
GOL
501
A
CRY
502
3
GOL
GOL
502
A
CRY
503
3
GOL
GOL
503
A
CRY
504
3
GOL
GOL
504
A
HOH
1
4
HOH
HOH
505
A
HOH
2
4
HOH
HOH
506
A
HOH
3
4
HOH
HOH
507
A
HOH
4
4
HOH
HOH
508
A
HOH
5
4
HOH
HOH
509
A
HOH
6
4
HOH
HOH
510
A
HOH
7
4
HOH
HOH
511
A
HOH
8
4
HOH
HOH
512
A
HOH
9
4
HOH
HOH
513
A
HOH
10
4
HOH
HOH
514
A
HOH
11
4
HOH
HOH
515
A
HOH
12
4
HOH
HOH
516
A
HOH
13
4
HOH
HOH
517
A
HOH
14
4
HOH
HOH
518
A
HOH
15
4
HOH
HOH
519
A
HOH
16
4
HOH
HOH
520
A
HOH
17
4
HOH
HOH
521
A
HOH
18
4
HOH
HOH
522
A
HOH
19
4
HOH
HOH
523
A
HOH
20
4
HOH
HOH
524
A
HOH
21
4
HOH
HOH
525
A
HOH
22
4
HOH
HOH
526
A
HOH
23
4
HOH
HOH
527
A
HOH
24
4
HOH
HOH
528
A
HOH
25
4
HOH
HOH
529
A
HOH
26
4
HOH
HOH
530
A
HOH
27
4
HOH
HOH
531
A
HOH
28
4
HOH
HOH
532
A
HOH
29
4
HOH
HOH
533
A
HOH
30
4
HOH
HOH
534
A
HOH
31
4
HOH
HOH
535
A
HOH
32
4
HOH
HOH
536
A
HOH
33
4
HOH
HOH
537
A
HOH
34
4
HOH
HOH
538
A
HOH
35
4
HOH
HOH
539
A
HOH
36
4
HOH
HOH
540
A
HOH
37
4
HOH
HOH
541
A
HOH
38
4
HOH
HOH
542
A
HOH
39
4
HOH
HOH
543
A
HOH
40
4
HOH
HOH
544
A
HOH
41
4
HOH
HOH
545
A
HOH
42
4
HOH
HOH
546
A
HOH
43
4
HOH
HOH
547
A
HOH
44
4
HOH
HOH
548
A
HOH
45
4
HOH
HOH
549
A
HOH
46
4
HOH
HOH
550
A
HOH
47
4
HOH
HOH
551
A
HOH
48
4
HOH
HOH
552
A
HOH
49
4
HOH
HOH
553
A
HOH
50
4
HOH
HOH
554
A
HOH
51
4
HOH
HOH
555
A
HOH
52
4
HOH
HOH
556
A
HOH
53
4
HOH
HOH
557
A
HOH
54
4
HOH
HOH
558
A
HOH
55
4
HOH
HOH
559
A
HOH
56
4
HOH
HOH
560
A
HOH
57
4
HOH
HOH
561
A
HOH
58
4
HOH
HOH
562
A
HOH
59
4
HOH
HOH
563
A
HOH
60
4
HOH
HOH
564
A
HOH
61
4
HOH
HOH
565
A
HOH
62
4
HOH
HOH
566
A
HOH
63
4
HOH
HOH
567
A
HOH
64
4
HOH
HOH
568
A
HOH
65
4
HOH
HOH
569
A
HOH
66
4
HOH
HOH
570
A
HOH
67
4
HOH
HOH
571
A
HOH
68
4
HOH
HOH
572
A
HOH
69
4
HOH
HOH
573
A
HOH
70
4
HOH
HOH
574
A
HOH
71
4
HOH
HOH
575
A
HOH
72
4
HOH
HOH
576
A
HOH
73
4
HOH
HOH
577
A
HOH
74
4
HOH
HOH
578
A
HOH
75
4
HOH
HOH
579
A
HOH
76
4
HOH
HOH
580
A
HOH
77
4
HOH
HOH
581
A
HOH
78
4
HOH
HOH
582
A
HOH
79
4
HOH
HOH
583
A
HOH
80
4
HOH
HOH
584
A
HOH
81
4
HOH
HOH
585
A
HOH
82
4
HOH
HOH
586
A
HOH
83
4
HOH
HOH
587
A
HOH
84
4
HOH
HOH
588
A
HOH
85
4
HOH
HOH
589
A
HOH
86
4
HOH
HOH
590
A
HOH
87
4
HOH
HOH
591
A
HOH
88
4
HOH
HOH
592
A
HOH
89
4
HOH
HOH
593
A
HOH
90
4
HOH
HOH
594
A
HOH
91
4
HOH
HOH
595
A
HOH
92
4
HOH
HOH
596
A
HOH
93
4
HOH
HOH
597
A
HOH
94
4
HOH
HOH
598
A
HOH
95
4
HOH
HOH
599
A
HOH
96
4
HOH
HOH
600
A
HOH
97
4
HOH
HOH
601
A
HOH
98
4
HOH
HOH
602
A
HOH
99
4
HOH
HOH
603
A
HOH
100
4
HOH
HOH
604
A
HOH
101
4
HOH
HOH
605
A
HOH
102
4
HOH
HOH
606
A
HOH
103
4
HOH
HOH
607
A
HOH
104
4
HOH
HOH
608
A
HOH
105
4
HOH
HOH
609
A
HOH
106
4
HOH
HOH
610
A
HOH
107
4
HOH
HOH
611
A
HOH
108
4
HOH
HOH
612
A
HOH
109
4
HOH
HOH
613
A
HOH
110
4
HOH
HOH
614
A
HOH
111
4
HOH
HOH
615
A
HOH
112
4
HOH
HOH
616
A
HOH
114
4
HOH
HOH
617
A
HOH
115
4
HOH
HOH
618
A
HOH
116
4
HOH
HOH
619
A
HOH
117
4
HOH
HOH
620
A
HOH
118
4
HOH
HOH
621
A
HOH
119
4
HOH
HOH
622
A
HOH
120
4
HOH
HOH
623
A
HOH
121
4
HOH
HOH
624
A
HOH
122
4
HOH
HOH
625
A
HOH
123
4
HOH
HOH
626
A
HOH
124
4
HOH
HOH
627
A
HOH
125
4
HOH
HOH
628
A
HOH
126
4
HOH
HOH
629
A
HOH
127
4
HOH
HOH
630
A
HOH
128
4
HOH
HOH
631
A
HOH
129
4
HOH
HOH
632
A
HOH
130
4
HOH
HOH
633
A
HOH
131
4
HOH
HOH
634
A
HOH
132
4
HOH
HOH
635
A
HOH
133
4
HOH
HOH
636
A
HOH
134
4
HOH
HOH
637
A
HOH
135
4
HOH
HOH
638
A
HOH
136
4
HOH
HOH
639
A
HOH
137
4
HOH
HOH
640
A
HOH
138
4
HOH
HOH
641
A
HOH
139
4
HOH
HOH
642
A
HOH
140
4
HOH
HOH
643
A
HOH
141
4
HOH
HOH
644
A
HOH
142
4
HOH
HOH
645
A
HOH
143
4
HOH
HOH
646
A
HOH
144
4
HOH
HOH
647
A
HOH
145
4
HOH
HOH
648
A
SER
2
n
1
SER
2
A
ALA
3
n
2
ALA
3
A
ALA
4
n
3
ALA
4
A
PRO
5
n
4
PRO
5
A
SER
6
n
5
SER
6
A
VAL
7
n
6
VAL
7
A
PHE
8
n
7
PHE
8
A
LEU
9
n
8
LEU
9
A
ILE
10
n
9
ILE
10
A
ASP
11
n
10
ASP
11
A
ASP
12
n
11
ASP
12
A
ASP
13
n
12
ASP
13
A
ARG
14
n
13
ARG
14
A
ASP
15
n
14
ASP
15
A
LEU
16
n
15
LEU
16
A
ARG
17
n
16
ARG
17
A
LYS
18
n
17
LYS
18
A
ALA
19
n
18
ALA
19
A
MET
20
n
19
MET
20
A
GLN
21
n
20
GLN
21
A
GLN
22
n
21
GLN
22
A
THR
23
n
22
THR
23
A
LEU
24
n
23
LEU
24
A
GLU
25
n
24
GLU
25
A
LEU
26
n
25
LEU
26
A
ALA
27
n
26
ALA
27
A
GLY
28
n
27
GLY
28
A
PHE
29
n
28
PHE
29
A
THR
30
n
29
THR
30
A
VAL
31
n
30
VAL
31
A
SER
32
n
31
SER
32
A
SER
33
n
32
SER
33
A
PHE
34
n
33
PHE
34
A
ALA
35
n
34
ALA
35
A
SER
36
n
35
SER
36
A
ALA
37
n
36
ALA
37
A
THR
38
n
37
THR
38
A
GLU
39
n
38
GLU
39
A
ALA
40
n
39
ALA
40
A
LEU
41
n
40
LEU
41
A
ALA
42
n
41
ALA
42
A
GLY
43
n
42
GLY
43
A
LEU
44
n
43
LEU
44
A
SER
45
n
44
SER
45
A
ALA
46
n
45
ALA
46
A
ASP
47
n
46
ASP
47
A
PHE
48
n
47
PHE
48
A
ALA
49
n
48
ALA
49
A
GLY
50
n
49
GLY
50
A
ILE
51
n
50
ILE
51
A
VAL
52
n
51
VAL
52
A
ILE
53
n
52
ILE
53
A
SER
54
n
53
SER
54
A
ASP
55
n
54
ASP
55
A
ILE
56
n
55
ILE
56
A
ARG
57
n
56
ARG
57
A
MET
58
n
57
MET
58
A
PRO
59
n
58
PRO
59
A
GLY
60
n
59
GLY
60
A
MET
61
n
60
MET
61
A
ASP
62
n
61
ASP
62
A
GLY
63
n
62
GLY
63
A
LEU
64
n
63
LEU
64
A
ALA
65
n
64
ALA
65
A
LEU
66
n
65
LEU
66
A
PHE
67
n
66
PHE
67
A
ARG
68
n
67
ARG
68
A
LYS
69
n
68
LYS
69
A
ILE
70
n
69
ILE
70
A
LEU
71
n
70
LEU
71
A
ALA
72
n
71
ALA
72
A
LEU
73
n
72
LEU
73
A
ASP
74
n
73
ASP
74
A
PRO
75
n
74
PRO
75
A
ASP
76
n
75
ASP
76
A
LEU
77
n
76
LEU
77
A
PRO
78
n
77
PRO
78
A
MET
79
n
78
MET
79
A
ILE
80
n
79
ILE
80
A
LEU
81
n
80
LEU
81
A
VAL
82
n
81
VAL
82
A
THR
83
n
82
THR
83
A
GLY
84
n
83
GLY
84
A
HIS
85
n
84
HIS
85
A
GLY
86
n
85
GLY
86
A
ASP
87
n
86
ASP
87
A
ILE
88
n
87
ILE
88
A
PRO
89
n
88
PRO
89
A
MET
90
n
89
MET
90
A
ALA
91
n
90
ALA
91
A
VAL
92
n
91
VAL
92
A
GLN
93
n
92
GLN
93
A
ALA
94
n
93
ALA
94
A
ILE
95
n
94
ILE
95
A
GLN
96
n
95
GLN
96
A
ASP
97
n
96
ASP
97
A
GLY
98
n
97
GLY
98
A
ALA
99
n
98
ALA
99
A
TYR
100
n
99
TYR
100
A
ASP
101
n
100
ASP
101
A
PHE
102
n
101
PHE
102
A
ILE
103
n
102
ILE
103
A
ALA
104
n
103
ALA
104
A
LYS
105
n
104
LYS
105
A
PRO
106
n
105
PRO
106
A
PHE
107
n
106
PHE
107
A
ALA
108
n
107
ALA
108
A
ALA
109
n
108
ALA
109
A
ASP
110
n
109
ASP
110
A
ARG
111
n
110
ARG
111
A
LEU
112
n
111
LEU
112
A
VAL
113
n
112
VAL
113
A
GLN
114
n
113
GLN
114
A
SER
115
n
114
SER
115
A
ALA
116
n
115
ALA
116
A
ARG
117
n
116
ARG
117
A
ARG
118
n
117
ARG
118
A
ALA
119
n
118
ALA
119
A
GLU
120
n
119
GLU
120
A
LYS
121
n
120
LYS
121
A
LYS
122
n
121
LYS
122
A
ARG
123
n
122
ARG
123
A
ARG
124
n
123
ARG
124
A
LEU
125
n
124
LEU
125
A
VAL
126
n
125
VAL
126
A
MET
127
n
126
MET
127
A
GLU
128
n
127
GLU
128
A
ASN
129
n
128
ASN
129
A
ARG
130
n
129
ARG
130
A
SER
131
n
130
SER
131
A
LEU
132
n
131
LEU
132
A
ARG
133
n
132
ARG
133
A
ARG
134
n
133
ARG
134
A
ALA
135
n
134
ALA
135
A
ALA
136
n
135
ALA
136
A
GLU
137
n
136
GLU
137
A
ALA
138
n
137
ALA
138
A
ALA
139
n
138
ALA
139
A
SER
140
n
139
SER
140
A
GLU
141
n
140
GLU
141
A
GLY
142
n
141
GLY
142
A
LEU
143
n
142
LEU
143
A
ALA
144
n
143
LYS
144
A
ALA
145
n
144
LEU
145
A
ALA
146
n
145
ALA
146
A
ALA
147
n
146
ALA
147
A
n
147
148
A
n
148
149
A
n
149
150
A
n
150
151
A
n
151
152
A
n
152
153
A
n
153
154
A
n
154
155
A
n
155
156
A
author_defined_assembly
2
dimeric
software_defined_assembly
PISA,PQS
4
tetrameric
10020
-35
25400
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_565
-x,-y+1,z
crystal symmetry operation
0.0000000000
58.1390000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
3_555
-x,y,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
4_565
x,-y+1,-z
crystal symmetry operation
0.0000000000
58.1390000000
0.0000000000
A
O
SER
32
A
O
SER
31
A
N
VAL
7
A
N
VAL
6
A
N
ILE
10
A
N
ILE
9
A
O
ILE
53
A
O
ILE
52
A
N
VAL
52
A
N
VAL
51
A
O
ILE
80
A
O
ILE
79
A
N
THR
83
A
N
THR
82
A
O
ILE
103
A
O
ILE
102
1
A
SO4
201
B
SO4
1
A
HOH
574
G
HOH
1
A
HOH
578
G
HOH
1
A
CG
LYS
144
A
CG
LYS
143
1
Y
1
A
CD
LYS
144
A
CD
LYS
143
1
Y
1
A
CE
LYS
144
A
CE
LYS
143
1
Y
1
A
NZ
LYS
144
A
NZ
LYS
143
1
Y
1
A
CG
LEU
145
A
CG
LEU
144
1
Y
1
A
CD1
LEU
145
A
CD1
LEU
144
1
Y
1
A
CD2
LEU
145
A
CD2
LEU
144
1
Y
1
A
ALA
148
A
ALA
147
1
Y
1
A
LEU
149
A
LEU
148
1
Y
1
A
GLU
150
A
GLU
149
1
Y
1
A
HIS
151
A
HIS
150
1
Y
1
A
HIS
152
A
HIS
151
1
Y
1
A
HIS
153
A
HIS
152
1
Y
1
A
HIS
154
A
HIS
153
1
Y
1
A
HIS
155
A
HIS
154
1
Y
1
A
HIS
156
A
HIS
155
1
Y
1
A
A
ND2
ND2
ASN
ASN
129
129
1.59
1_555
2_565
1
A
ASP
74
-172.85
106.55
PROTEIN_REP1.PARAM
WATER.PARAM
ION.PARAM
CRY.PARAM
22.4
-0.67
0.00
0.00
-1.10
0.00
1.77
0.232
0.005
0.196
2.00
36.70
1897
19264
19264
9.8
98.8
RANDOM
215180.43
0.000000
1
RESTRAINED
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
PDB ENTRY 1QKK
Engh & Huber
FLAT MODEL
66.2093
0.385197
0.25
0.21
5.00
0.19
0.19
2.00
36.70
144
1263
29
0
1090
0.015
1.7
21.9
0.99
2.41
1.50
2.96
2.00
4.00
2.00
4.92
2.50
0.259
0.015
0.246
2.13
318
2818
6
10.1
98.4
16.6
2.0
36.7
1L5Z
19264
19264
2.2
0.061
1
7.1
3.04
98.6
0.222
2.0
2.07
2.2
3548
1
1.61
97.5
data collection
CrystalClear
data reduction
d*TREK
phasing
AMoRE
refinement
CNS
1.0
data reduction
CrystalClear
(MSC/RIGAKU)
data scaling
d*TREK
CRYSTAL STRUCTURE OF THE E121K SUBSTITUTION OF THE RECEIVER DOMAIN OF SINORHIZOBIUM MELILOTI DCTD
1
N
N
2
N
N
3
N
N
3
N
N
3
N
N
3
N
N
4
N
N
analytical ultracentrifuge data indicates solution form is a dimer;
genetic and biochemical data indicates substitution destabilizes the dimer ~20-fold, leading to 'derepression' of the ATPase domain
asymmetric unit is a monomer
biological unit is a dimer - build with symmetry operation -X, -Y, Z
A
ASP
13
A
ASP
12
HELX_P
A
LEU
26
A
LEU
25
1
1
14
A
SER
36
A
SER
35
HELX_P
A
GLY
43
A
GLY
42
1
2
8
A
ASP
62
A
ASP
61
HELX_P
A
ASP
74
A
ASP
73
1
3
13
A
GLY
84
A
GLY
83
HELX_P
A
GLY
86
A
GLY
85
5
4
3
A
ASP
87
A
ASP
86
HELX_P
A
ASP
97
A
ASP
96
1
5
11
A
ALA
108
A
ALA
107
HELX_P
A
ALA
147
A
ALA
146
1
6
40
covale
1.462
none
A
SO4
201
B
S
SO4
1_555
A
SO4
201
B
O1
SO4
1_555
covale
1.464
none
A
SO4
201
B
S
SO4
1_555
A
SO4
201
B
O2
SO4
1_555
covale
1.470
none
A
SO4
201
B
S
SO4
1_555
A
SO4
201
B
O3
SO4
1_555
covale
1.477
none
A
SO4
201
B
S
SO4
1_555
A
SO4
201
B
O4
SO4
1_555
TRANSCRIPTION REGULATOR
two component receiver domain, sigma 54, regulator of AAA+ ATPase, TRANSCRIPTION REGULATOR
A
LYS
105
A
LYS
104
1
A
PRO
106
A
PRO
105
-0.59
DCTD_RHIME
UNP
1
1
P13632
MSAAPSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILALDPDLPMI
LVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKRRLVMENRSLRRAAEAASEGL
2
143
1L5Z
2
143
P13632
A
1
1
142
1
GLU
engineered mutation
LYS
121
1L5Z
A
P13632
UNP
121
120
1
expression tag
LYS
144
1L5Z
A
P13632
UNP
143
1
expression tag
LEU
145
1L5Z
A
P13632
UNP
144
1
expression tag
ALA
146
1L5Z
A
P13632
UNP
145
1
expression tag
ALA
147
1L5Z
A
P13632
UNP
146
1
expression tag
ALA
148
1L5Z
A
P13632
UNP
147
1
expression tag
LEU
149
1L5Z
A
P13632
UNP
148
1
expression tag
GLU
150
1L5Z
A
P13632
UNP
149
1
expression tag
HIS
151
1L5Z
A
P13632
UNP
150
1
expression tag
HIS
152
1L5Z
A
P13632
UNP
151
1
expression tag
HIS
153
1L5Z
A
P13632
UNP
152
1
expression tag
HIS
154
1L5Z
A
P13632
UNP
153
1
expression tag
HIS
155
1L5Z
A
P13632
UNP
154
1
expression tag
HIS
156
1L5Z
A
P13632
UNP
155
5
parallel
parallel
parallel
parallel
A
THR
30
A
THR
29
A
PHE
34
A
PHE
33
A
SER
6
A
SER
5
A
ILE
10
A
ILE
9
A
ILE
51
A
ILE
50
A
ASP
55
A
ASP
54
A
MET
79
A
MET
78
A
THR
83
A
THR
82
A
ASP
101
A
ASP
100
A
ALA
104
A
ALA
103
BINDING SITE FOR RESIDUE SO4 A 201
A
SO4
201
Software
6
BINDING SITE FOR RESIDUE GOL A 501
A
GOL
501
Software
5
BINDING SITE FOR RESIDUE GOL A 502
A
GOL
502
Software
5
BINDING SITE FOR RESIDUE GOL A 503
A
GOL
503
Software
8
BINDING SITE FOR RESIDUE GOL A 504
A
GOL
504
Software
5
A
ARG
14
A
ARG
13
6
1_555
A
ARG
14
A
ARG
13
6
2_555
A
ARG
17
A
ARG
16
6
2_555
A
ARG
17
A
ARG
16
6
1_555
A
HOH
574
G
HOH
6
2_555
A
HOH
574
G
HOH
6
1_555
A
ARG
57
A
ARG
56
5
1_555
A
GLY
84
A
GLY
83
5
1_555
A
HIS
85
A
HIS
84
5
1_555
A
GLY
86
A
GLY
85
5
1_555
A
ASP
87
A
ASP
86
5
1_555
A
GLN
22
A
GLN
21
5
1_555
A
ARG
68
A
ARG
67
5
8_455
A
GLN
93
A
GLN
92
5
8_455
A
ALA
94
A
ALA
93
5
8_455
A
ASP
97
A
ASP
96
5
8_455
A
ILE
95
A
ILE
94
8
2_565
A
ASP
101
A
ASP
100
8
2_565
A
ARG
111
A
ARG
110
8
1_555
A
GLN
114
A
GLN
113
8
1_555
A
SER
115
A
SER
114
8
1_555
A
ARG
118
A
ARG
117
8
1_555
A
HOH
559
G
HOH
8
2_565
A
HOH
559
G
HOH
8
1_555
A
HIS
85
A
HIS
84
5
1_555
A
ILE
88
A
ILE
87
5
1_555
A
PRO
89
A
PRO
88
5
1_555
A
ARG
111
A
ARG
110
5
2_565
A
HOH
532
G
HOH
5
2_565
23
I 2 2 2