0.011331
0.000000
0.000000
0.000000
0.007017
0.000000
0.000000
0.000000
0.012644
0.00000
0.00000
0.00000
Stanger, F.V.
Schirmer, T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
88.250
142.520
79.090
C10 H15 N5 O10 P2
427.201
n
ADENOSINE-5'-DIPHOSPHATE
non-polymer
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
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
Mg 2
24.305
MAGNESIUM ION
non-polymer
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
N
1
N
P
N
2
N
O
N
3
N
O
N
4
N
O
N
5
S
P
N
6
N
O
N
7
N
O
N
8
N
O
N
9
N
O
N
10
N
C
N
11
R
C
N
12
N
O
N
13
S
C
N
14
N
O
N
15
R
C
N
16
N
O
N
17
R
C
Y
18
N
N
Y
19
N
C
Y
20
N
N
Y
21
N
C
Y
22
N
C
N
23
N
N
Y
24
N
N
Y
25
N
C
Y
26
N
N
Y
27
N
C
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
H
N
42
N
H
N
43
N
N
N
44
S
C
N
45
N
C
N
46
N
O
N
47
N
C
N
48
N
O
N
49
N
H
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
N
N
57
S
C
N
58
N
C
N
59
N
O
N
60
N
C
N
61
N
C
N
62
N
C
N
63
N
N
N
64
N
C
N
65
N
N
N
66
N
N
N
67
N
O
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
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
N
N
84
S
C
N
85
N
C
N
86
N
O
N
87
N
C
N
88
N
C
N
89
N
O
N
90
N
N
N
91
N
O
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
N
N
101
S
C
N
102
N
C
N
103
N
O
N
104
N
C
N
105
N
C
N
106
N
O
N
107
N
O
N
108
N
O
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
N
N
117
R
C
N
118
N
C
N
119
N
O
N
120
N
C
N
121
N
S
N
122
N
O
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
N
N
131
S
C
N
132
N
C
N
133
N
O
N
134
N
C
N
135
N
C
N
136
N
C
N
137
N
O
N
138
N
N
N
139
N
O
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
N
N
151
S
C
N
152
N
C
N
153
N
O
N
154
N
C
N
155
N
C
N
156
N
C
N
157
N
O
N
158
N
O
N
159
N
O
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
N
C
N
171
N
C
N
172
N
O
N
173
N
O
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
N
N
180
S
C
N
181
N
C
N
182
N
O
N
183
N
C
Y
184
N
C
Y
185
N
N
Y
186
N
C
Y
187
N
C
Y
188
N
N
N
189
N
O
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
O
N
201
N
H
N
202
N
H
N
203
N
N
N
204
S
C
N
205
N
C
N
206
N
O
N
207
S
C
N
208
N
C
N
209
N
C
N
210
N
C
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
N
N
226
S
C
N
227
N
C
N
228
N
O
N
229
N
C
N
230
N
C
N
231
N
C
N
232
N
C
N
233
N
O
N
234
N
H
N
235
N
H
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
N
252
N
C
N
253
N
C
N
254
N
C
N
255
N
N
N
256
N
O
N
257
N
H
N
258
N
H
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
H
N
271
N
H
N
272
N
N
N
273
S
C
N
274
N
C
N
275
N
O
N
276
N
C
N
277
N
C
N
278
N
S
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
H
N
291
N
H
N
292
N
MG
N
293
N
N
N
294
S
C
N
295
N
C
N
296
N
O
N
297
N
C
Y
298
N
C
Y
299
N
C
Y
300
N
C
Y
301
N
C
Y
302
N
C
Y
303
N
C
N
304
N
O
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
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
N
C
N
321
N
C
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
N
338
N
O
N
339
N
O
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
N
N
348
S
C
N
349
N
C
N
350
N
O
N
351
R
C
N
352
N
O
N
353
N
C
N
354
N
O
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
H
N
364
N
N
N
365
S
C
N
366
N
C
N
367
N
O
N
368
N
C
Y
369
N
C
Y
370
N
C
Y
371
N
C
Y
372
N
N
Y
373
N
C
Y
374
N
C
Y
375
N
C
Y
376
N
C
Y
377
N
C
N
378
N
O
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
N
N
392
S
C
N
393
N
C
N
394
N
O
N
395
N
C
Y
396
N
C
Y
397
N
C
Y
398
N
C
Y
399
N
C
Y
400
N
C
Y
401
N
C
N
402
N
O
N
403
N
O
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
N
N
416
S
C
N
417
N
C
N
418
N
O
N
419
N
C
N
420
N
C
N
421
N
C
N
422
N
O
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
H
N
1
N
doub
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
sing
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
Y
30
N
sing
Y
31
N
sing
Y
32
N
doub
N
33
N
sing
Y
34
N
sing
Y
35
N
sing
Y
36
N
doub
N
37
N
sing
Y
38
N
doub
N
39
N
sing
N
40
N
sing
Y
41
N
sing
Y
42
N
doub
N
43
N
sing
Y
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
doub
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
sing
N
62
N
sing
N
63
N
doub
N
64
N
sing
N
65
N
sing
N
66
N
sing
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
sing
N
77
N
doub
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
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
doub
N
95
N
sing
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
sing
N
104
N
sing
N
105
N
doub
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
doub
N
111
N
sing
N
112
N
sing
N
113
N
sing
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
doub
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
doub
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
doub
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
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
doub
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
doub
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
doub
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
Y
184
N
sing
Y
185
N
doub
Y
186
N
doub
N
187
N
sing
Y
188
N
sing
N
189
N
sing
Y
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
doub
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
doub
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
sing
N
242
N
sing
N
243
N
sing
N
244
N
doub
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
sing
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
doub
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
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
Y
292
N
doub
Y
293
N
sing
Y
294
N
sing
N
295
N
sing
Y
296
N
doub
N
297
N
sing
Y
298
N
doub
N
299
N
sing
Y
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
sing
N
309
N
sing
N
310
N
doub
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
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
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
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
doub
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
Y
361
N
doub
Y
362
N
sing
Y
363
N
sing
N
364
N
sing
Y
365
N
doub
Y
366
N
sing
Y
367
N
sing
N
368
N
sing
Y
369
N
sing
Y
370
N
doub
N
371
N
sing
Y
372
N
doub
N
373
N
sing
Y
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
N
383
N
sing
N
384
N
doub
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
Y
389
N
doub
Y
390
N
sing
Y
391
N
sing
N
392
N
sing
Y
393
N
doub
N
394
N
sing
Y
395
N
doub
N
396
N
sing
Y
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
doub
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
US
Plos One
1932-6203
9
e107289
e107289
10.1371/journal.pone.0107289
25202966
Structure of the N-Terminal Gyrase B Fragment in Complex with ADPPi Reveals Rigid-Body Motion Induced by ATP Hydrolysis
2014
10.2210/pdb4prv/pdb
pdb_00004prv
100
1
PIXEL
2012-09-03
DECTRIS PILATUS 2M
SINGLE WAVELENGTH
M
x-ray
1
1.0000
1.0
X06DA
SLS
1.0000
SYNCHROTRON
SLS BEAMLINE X06DA
44118.641
GyrB
5.99.1.3
UNP residues 2-392
1
man
polymer
427.201
ADENOSINE-5'-DIPHOSPHATE
1
syn
non-polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
18.015
water
126
nat
water
no
no
MHHHHHHSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDD
GRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPL
AVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKT
PIHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDD
AREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMT
MHHHHHHSNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDD
GRGIPTGIHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPL
AVTGETEKTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKT
PIHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDD
AREGLIAVVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMT
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
sample
562
Escherichia coli
562
Escherichia coli
BL21(DE3)
plasmid
pRSFDuet1
1
3.05
59.30
0.198
VAPOR DIFFUSION, SITTING DROP
8.5
10%(w/v) PEG20000, 20%(v/v) PEGMME550, 0.02M each carboxylic acid, 0.1M bicine/Trizma base pH 8.5, vapor diffusion, sitting drop, temperature 293.15K
293.15
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
struct_site
repository
Initial release
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
2014-09-24
1
1
2017-11-22
1
2
2023-11-08
_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
GyrB in complex with AMPPNP
GyrB in complex with ADP+Pi
RCSB
Y
PDBJ
2014-03-06
REL
REL
ADP
ADENOSINE-5'-DIPHOSPHATE
MG
MAGNESIUM ION
HOH
water
1EI1
PDB
experimental model
ADP
1
2
ADP
ADP
401
A
MG
2
3
MG
MG
402
A
HOH
1
4
HOH
HOH
501
A
HOH
2
4
HOH
HOH
502
A
HOH
3
4
HOH
HOH
503
A
HOH
4
4
HOH
HOH
504
A
HOH
5
4
HOH
HOH
505
A
HOH
6
4
HOH
HOH
506
A
HOH
7
4
HOH
HOH
507
A
HOH
8
4
HOH
HOH
508
A
HOH
9
4
HOH
HOH
509
A
HOH
10
4
HOH
HOH
510
A
HOH
11
4
HOH
HOH
511
A
HOH
12
4
HOH
HOH
512
A
HOH
13
4
HOH
HOH
513
A
HOH
14
4
HOH
HOH
514
A
HOH
15
4
HOH
HOH
515
A
HOH
16
4
HOH
HOH
516
A
HOH
17
4
HOH
HOH
517
A
HOH
18
4
HOH
HOH
518
A
HOH
19
4
HOH
HOH
519
A
HOH
20
4
HOH
HOH
520
A
HOH
21
4
HOH
HOH
521
A
HOH
22
4
HOH
HOH
522
A
HOH
23
4
HOH
HOH
523
A
HOH
24
4
HOH
HOH
524
A
HOH
25
4
HOH
HOH
525
A
HOH
26
4
HOH
HOH
526
A
HOH
27
4
HOH
HOH
527
A
HOH
28
4
HOH
HOH
528
A
HOH
29
4
HOH
HOH
529
A
HOH
30
4
HOH
HOH
530
A
HOH
31
4
HOH
HOH
531
A
HOH
32
4
HOH
HOH
532
A
HOH
33
4
HOH
HOH
533
A
HOH
34
4
HOH
HOH
534
A
HOH
35
4
HOH
HOH
535
A
HOH
36
4
HOH
HOH
536
A
HOH
37
4
HOH
HOH
537
A
HOH
38
4
HOH
HOH
538
A
HOH
39
4
HOH
HOH
539
A
HOH
40
4
HOH
HOH
540
A
HOH
41
4
HOH
HOH
541
A
HOH
42
4
HOH
HOH
542
A
HOH
43
4
HOH
HOH
543
A
HOH
44
4
HOH
HOH
544
A
HOH
45
4
HOH
HOH
545
A
HOH
46
4
HOH
HOH
546
A
HOH
47
4
HOH
HOH
547
A
HOH
48
4
HOH
HOH
548
A
HOH
49
4
HOH
HOH
549
A
HOH
50
4
HOH
HOH
550
A
HOH
51
4
HOH
HOH
551
A
HOH
52
4
HOH
HOH
552
A
HOH
53
4
HOH
HOH
553
A
HOH
54
4
HOH
HOH
554
A
HOH
55
4
HOH
HOH
555
A
HOH
56
4
HOH
HOH
556
A
HOH
57
4
HOH
HOH
557
A
HOH
58
4
HOH
HOH
558
A
HOH
59
4
HOH
HOH
559
A
HOH
60
4
HOH
HOH
560
A
HOH
61
4
HOH
HOH
561
A
HOH
62
4
HOH
HOH
562
A
HOH
63
4
HOH
HOH
563
A
HOH
64
4
HOH
HOH
564
A
HOH
65
4
HOH
HOH
565
A
HOH
66
4
HOH
HOH
566
A
HOH
67
4
HOH
HOH
567
A
HOH
68
4
HOH
HOH
568
A
HOH
69
4
HOH
HOH
569
A
HOH
70
4
HOH
HOH
570
A
HOH
71
4
HOH
HOH
571
A
HOH
72
4
HOH
HOH
572
A
HOH
73
4
HOH
HOH
573
A
HOH
74
4
HOH
HOH
574
A
HOH
75
4
HOH
HOH
575
A
HOH
76
4
HOH
HOH
576
A
HOH
77
4
HOH
HOH
577
A
HOH
78
4
HOH
HOH
578
A
HOH
79
4
HOH
HOH
579
A
HOH
80
4
HOH
HOH
580
A
HOH
81
4
HOH
HOH
581
A
HOH
82
4
HOH
HOH
582
A
HOH
83
4
HOH
HOH
583
A
HOH
84
4
HOH
HOH
584
A
HOH
85
4
HOH
HOH
585
A
HOH
86
4
HOH
HOH
586
A
HOH
87
4
HOH
HOH
587
A
HOH
89
4
HOH
HOH
588
A
HOH
90
4
HOH
HOH
589
A
HOH
91
4
HOH
HOH
590
A
HOH
92
4
HOH
HOH
591
A
HOH
93
4
HOH
HOH
592
A
HOH
94
4
HOH
HOH
593
A
HOH
95
4
HOH
HOH
594
A
HOH
96
4
HOH
HOH
595
A
HOH
97
4
HOH
HOH
596
A
HOH
98
4
HOH
HOH
597
A
HOH
99
4
HOH
HOH
598
A
HOH
100
4
HOH
HOH
599
A
HOH
101
4
HOH
HOH
600
A
HOH
102
4
HOH
HOH
601
A
HOH
104
4
HOH
HOH
602
A
HOH
105
4
HOH
HOH
603
A
HOH
106
4
HOH
HOH
604
A
HOH
107
4
HOH
HOH
605
A
HOH
109
4
HOH
HOH
606
A
HOH
110
4
HOH
HOH
607
A
HOH
111
4
HOH
HOH
608
A
HOH
112
4
HOH
HOH
609
A
HOH
113
4
HOH
HOH
610
A
HOH
114
4
HOH
HOH
611
A
HOH
115
4
HOH
HOH
612
A
HOH
116
4
HOH
HOH
613
A
HOH
117
4
HOH
HOH
614
A
HOH
118
4
HOH
HOH
615
A
HOH
119
4
HOH
HOH
616
A
HOH
120
4
HOH
HOH
617
A
HOH
121
4
HOH
HOH
618
A
HOH
122
4
HOH
HOH
619
A
HOH
123
4
HOH
HOH
620
A
HOH
124
4
HOH
HOH
621
A
HOH
125
4
HOH
HOH
622
A
HOH
126
4
HOH
HOH
623
A
HOH
127
4
HOH
HOH
624
A
HOH
128
4
HOH
HOH
625
A
HOH
129
4
HOH
HOH
626
A
3.500
3.500
75.030
75.030
n
1
-5
A
n
2
-4
A
n
3
-3
A
n
4
-2
A
n
5
-1
A
n
6
0
A
n
7
1
A
n
8
2
A
n
9
3
A
n
10
4
A
TYR
5
n
11
TYR
5
A
ASP
6
n
12
ASP
6
A
SER
7
n
13
SER
7
A
SER
8
n
14
SER
8
A
SER
9
n
15
SER
9
A
ILE
10
n
16
ILE
10
A
LYS
11
n
17
LYS
11
A
VAL
12
n
18
VAL
12
A
LEU
13
n
19
LEU
13
A
LYS
14
n
20
LYS
14
A
GLY
15
n
21
GLY
15
A
LEU
16
n
22
LEU
16
A
ASP
17
n
23
ASP
17
A
ALA
18
n
24
ALA
18
A
VAL
19
n
25
VAL
19
A
ARG
20
n
26
ARG
20
A
LYS
21
n
27
LYS
21
A
ARG
22
n
28
ARG
22
A
PRO
23
n
29
PRO
23
A
GLY
24
n
30
GLY
24
A
MET
25
n
31
MET
25
A
TYR
26
n
32
TYR
26
A
ILE
27
n
33
ILE
27
A
GLY
28
n
34
GLY
28
A
ASP
29
n
35
ASP
29
A
THR
30
n
36
THR
30
A
ASP
31
n
37
ASP
31
A
ASP
32
n
38
ASP
32
A
GLY
33
n
39
GLY
33
A
THR
34
n
40
THR
34
A
GLY
35
n
41
GLY
35
A
LEU
36
n
42
LEU
36
A
HIS
37
n
43
HIS
37
A
HIS
38
n
44
HIS
38
A
MET
39
n
45
MET
39
A
VAL
40
n
46
VAL
40
A
PHE
41
n
47
PHE
41
A
GLU
42
n
48
GLU
42
A
VAL
43
n
49
VAL
43
A
VAL
44
n
50
VAL
44
A
ASP
45
n
51
ASP
45
A
ASN
46
n
52
ASN
46
A
ALA
47
n
53
ALA
47
A
ILE
48
n
54
ILE
48
A
ASP
49
n
55
ASP
49
A
GLU
50
n
56
GLU
50
A
ALA
51
n
57
ALA
51
A
LEU
52
n
58
LEU
52
A
ALA
53
n
59
ALA
53
A
GLY
54
n
60
GLY
54
A
HIS
55
n
61
HIS
55
A
CYS
56
n
62
CYS
56
A
LYS
57
n
63
LYS
57
A
GLU
58
n
64
GLU
58
A
ILE
59
n
65
ILE
59
A
ILE
60
n
66
ILE
60
A
VAL
61
n
67
VAL
61
A
THR
62
n
68
THR
62
A
ILE
63
n
69
ILE
63
A
HIS
64
n
70
HIS
64
A
ALA
65
n
71
ALA
65
A
ASP
66
n
72
ASP
66
A
ASN
67
n
73
ASN
67
A
SER
68
n
74
SER
68
A
VAL
69
n
75
VAL
69
A
SER
70
n
76
SER
70
A
VAL
71
n
77
VAL
71
A
GLN
72
n
78
GLN
72
A
ASP
73
n
79
ASP
73
A
ASP
74
n
80
ASP
74
A
GLY
75
n
81
GLY
75
A
ARG
76
n
82
ARG
76
A
GLY
77
n
83
GLY
77
A
ILE
78
n
84
ILE
78
A
PRO
79
n
85
PRO
79
A
THR
80
n
86
THR
80
A
GLY
81
n
87
GLY
81
A
ILE
82
n
88
ILE
82
A
HIS
83
n
89
HIS
83
A
PRO
84
n
90
PRO
84
A
GLU
85
n
91
GLU
85
A
GLU
86
n
92
GLU
86
A
GLY
87
n
93
GLY
87
A
VAL
88
n
94
VAL
88
A
SER
89
n
95
SER
89
A
ALA
90
n
96
ALA
90
A
ALA
91
n
97
ALA
91
A
GLU
92
n
98
GLU
92
A
VAL
93
n
99
VAL
93
A
ILE
94
n
100
ILE
94
A
MET
95
n
101
MET
95
A
THR
96
n
102
THR
96
A
VAL
97
n
103
VAL
97
A
LEU
98
n
104
LEU
98
A
HIS
99
n
105
HIS
99
A
ALA
100
n
106
ALA
100
A
GLY
101
n
107
GLY
101
A
GLY
102
n
108
GLY
102
A
LYS
103
n
109
LYS
103
A
PHE
104
n
110
PHE
104
A
ASP
105
n
111
ASP
105
A
ASP
106
n
112
ASP
106
A
ASN
107
n
113
ASN
107
A
SER
108
n
114
SER
108
A
TYR
109
n
115
TYR
109
A
LYS
110
n
116
LYS
110
A
VAL
111
n
117
VAL
111
A
SER
112
n
118
SER
112
A
GLY
113
n
119
GLY
113
A
GLY
114
n
120
GLY
114
A
LEU
115
n
121
LEU
115
A
HIS
116
n
122
HIS
116
A
GLY
117
n
123
GLY
117
A
VAL
118
n
124
VAL
118
A
GLY
119
n
125
GLY
119
A
VAL
120
n
126
VAL
120
A
SER
121
n
127
SER
121
A
VAL
122
n
128
VAL
122
A
VAL
123
n
129
VAL
123
A
ASN
124
n
130
ASN
124
A
ALA
125
n
131
ALA
125
A
LEU
126
n
132
LEU
126
A
SER
127
n
133
SER
127
A
GLN
128
n
134
GLN
128
A
LYS
129
n
135
LYS
129
A
LEU
130
n
136
LEU
130
A
GLU
131
n
137
GLU
131
A
LEU
132
n
138
LEU
132
A
VAL
133
n
139
VAL
133
A
ILE
134
n
140
ILE
134
A
GLN
135
n
141
GLN
135
A
ARG
136
n
142
ARG
136
A
GLU
137
n
143
GLU
137
A
GLY
138
n
144
GLY
138
A
LYS
139
n
145
LYS
139
A
ILE
140
n
146
ILE
140
A
HIS
141
n
147
HIS
141
A
ARG
142
n
148
ARG
142
A
GLN
143
n
149
GLN
143
A
ILE
144
n
150
ILE
144
A
TYR
145
n
151
TYR
145
A
GLU
146
n
152
GLU
146
A
HIS
147
n
153
HIS
147
A
GLY
148
n
154
GLY
148
A
VAL
149
n
155
VAL
149
A
PRO
150
n
156
PRO
150
A
GLN
151
n
157
GLN
151
A
ALA
152
n
158
ALA
152
A
PRO
153
n
159
PRO
153
A
LEU
154
n
160
LEU
154
A
ALA
155
n
161
ALA
155
A
VAL
156
n
162
VAL
156
A
THR
157
n
163
THR
157
A
GLY
158
n
164
GLY
158
A
GLU
159
n
165
GLU
159
A
THR
160
n
166
THR
160
A
GLU
161
n
167
GLU
161
A
LYS
162
n
168
LYS
162
A
THR
163
n
169
THR
163
A
GLY
164
n
170
GLY
164
A
THR
165
n
171
THR
165
A
MET
166
n
172
MET
166
A
VAL
167
n
173
VAL
167
A
ARG
168
n
174
ARG
168
A
PHE
169
n
175
PHE
169
A
TRP
170
n
176
TRP
170
A
PRO
171
n
177
PRO
171
A
SER
172
n
178
SER
172
A
LEU
173
n
179
LEU
173
A
GLU
174
n
180
GLU
174
A
THR
175
n
181
THR
175
A
PHE
176
n
182
PHE
176
A
THR
177
n
183
THR
177
A
ASN
178
n
184
ASN
178
A
VAL
179
n
185
VAL
179
A
THR
180
n
186
THR
180
A
GLU
181
n
187
GLU
181
A
PHE
182
n
188
PHE
182
A
GLU
183
n
189
GLU
183
A
TYR
184
n
190
TYR
184
A
GLU
185
n
191
GLU
185
A
ILE
186
n
192
ILE
186
A
LEU
187
n
193
LEU
187
A
ALA
188
n
194
ALA
188
A
LYS
189
n
195
LYS
189
A
ARG
190
n
196
ARG
190
A
LEU
191
n
197
LEU
191
A
ARG
192
n
198
ARG
192
A
GLU
193
n
199
GLU
193
A
LEU
194
n
200
LEU
194
A
SER
195
n
201
SER
195
A
PHE
196
n
202
PHE
196
A
LEU
197
n
203
LEU
197
A
ASN
198
n
204
ASN
198
A
SER
199
n
205
SER
199
A
GLY
200
n
206
GLY
200
A
VAL
201
n
207
VAL
201
A
SER
202
n
208
SER
202
A
ILE
203
n
209
ILE
203
A
ARG
204
n
210
ARG
204
A
LEU
205
n
211
LEU
205
A
ARG
206
n
212
ARG
206
A
ASP
207
n
213
ASP
207
A
LYS
208
n
214
LYS
208
A
ARG
209
n
215
ARG
209
A
ASP
210
n
216
ASP
210
A
GLY
211
n
217
GLY
211
A
LYS
212
n
218
LYS
212
A
GLU
213
n
219
GLU
213
A
ASP
214
n
220
ASP
214
A
HIS
215
n
221
HIS
215
A
PHE
216
n
222
PHE
216
A
HIS
217
n
223
HIS
217
A
TYR
218
n
224
TYR
218
A
GLU
219
n
225
GLU
219
A
GLY
220
n
226
GLY
220
A
GLY
221
n
227
GLY
221
A
ILE
222
n
228
ILE
222
A
LYS
223
n
229
LYS
223
A
ALA
224
n
230
ALA
224
A
PHE
225
n
231
PHE
225
A
VAL
226
n
232
VAL
226
A
GLU
227
n
233
GLU
227
A
TYR
228
n
234
TYR
228
A
LEU
229
n
235
LEU
229
A
ASN
230
n
236
ASN
230
A
LYS
231
n
237
LYS
231
A
ASN
232
n
238
ASN
232
A
LYS
233
n
239
LYS
233
A
THR
234
n
240
THR
234
A
PRO
235
n
241
PRO
235
A
ILE
236
n
242
ILE
236
A
HIS
237
n
243
HIS
237
A
PRO
238
n
244
PRO
238
A
ASN
239
n
245
ASN
239
A
ILE
240
n
246
ILE
240
A
PHE
241
n
247
PHE
241
A
TYR
242
n
248
TYR
242
A
PHE
243
n
249
PHE
243
A
SER
244
n
250
SER
244
A
THR
245
n
251
THR
245
A
GLU
246
n
252
GLU
246
A
LYS
247
n
253
LYS
247
A
ASP
248
n
254
ASP
248
A
GLY
249
n
255
GLY
249
A
ILE
250
n
256
ILE
250
A
GLY
251
n
257
GLY
251
A
VAL
252
n
258
VAL
252
A
GLU
253
n
259
GLU
253
A
VAL
254
n
260
VAL
254
A
ALA
255
n
261
ALA
255
A
LEU
256
n
262
LEU
256
A
GLN
257
n
263
GLN
257
A
TRP
258
n
264
TRP
258
A
ASN
259
n
265
ASN
259
A
ASP
260
n
266
ASP
260
A
GLY
261
n
267
GLY
261
A
PHE
262
n
268
PHE
262
A
GLN
263
n
269
GLN
263
A
GLU
264
n
270
GLU
264
A
ASN
265
n
271
ASN
265
A
ILE
266
n
272
ILE
266
A
TYR
267
n
273
TYR
267
A
CYS
268
n
274
CYS
268
A
PHE
269
n
275
PHE
269
A
THR
270
n
276
THR
270
A
ASN
271
n
277
ASN
271
A
ASN
272
n
278
ASN
272
A
ILE
273
n
279
ILE
273
A
PRO
274
n
280
PRO
274
A
GLN
275
n
281
GLN
275
A
ARG
276
n
282
ARG
276
A
ASP
277
n
283
ASP
277
A
GLY
278
n
284
GLY
278
A
GLY
279
n
285
GLY
279
A
THR
280
n
286
THR
280
A
HIS
281
n
287
HIS
281
A
LEU
282
n
288
LEU
282
A
ALA
283
n
289
ALA
283
A
GLY
284
n
290
GLY
284
A
PHE
285
n
291
PHE
285
A
ARG
286
n
292
ARG
286
A
ALA
287
n
293
ALA
287
A
ALA
288
n
294
ALA
288
A
MET
289
n
295
MET
289
A
THR
290
n
296
THR
290
A
ARG
291
n
297
ARG
291
A
THR
292
n
298
THR
292
A
LEU
293
n
299
LEU
293
A
ASN
294
n
300
ASN
294
A
ALA
295
n
301
ALA
295
A
TYR
296
n
302
TYR
296
A
MET
297
n
303
MET
297
A
ASP
298
n
304
ASP
298
A
LYS
299
n
305
LYS
299
A
GLU
300
n
306
GLU
300
A
GLY
301
n
307
GLY
301
A
TYR
302
n
308
TYR
302
A
n
309
303
A
n
310
304
A
n
311
305
A
n
312
306
A
n
313
307
A
n
314
308
A
n
315
309
A
n
316
310
A
n
317
311
A
n
318
312
A
n
319
313
A
n
320
314
A
n
321
315
A
ARG
316
n
322
ARG
316
A
GLU
317
n
323
GLU
317
A
GLY
318
n
324
GLY
318
A
LEU
319
n
325
LEU
319
A
ILE
320
n
326
ILE
320
A
ALA
321
n
327
ALA
321
A
VAL
322
n
328
VAL
322
A
VAL
323
n
329
VAL
323
A
SER
324
n
330
SER
324
A
VAL
325
n
331
VAL
325
A
LYS
326
n
332
LYS
326
A
VAL
327
n
333
VAL
327
A
PRO
328
n
334
PRO
328
A
ASP
329
n
335
ASP
329
A
PRO
330
n
336
PRO
330
A
LYS
331
n
337
LYS
331
A
PHE
332
n
338
PHE
332
A
SER
333
n
339
SER
333
A
SER
334
n
340
SER
334
A
GLN
335
n
341
GLN
335
A
THR
336
n
342
THR
336
A
LYS
337
n
343
LYS
337
A
ASP
338
n
344
ASP
338
A
LYS
339
n
345
LYS
339
A
LEU
340
n
346
LEU
340
A
VAL
341
n
347
VAL
341
A
SER
342
n
348
SER
342
A
SER
343
n
349
SER
343
A
GLU
344
n
350
GLU
344
A
VAL
345
n
351
VAL
345
A
LYS
346
n
352
LYS
346
A
SER
347
n
353
SER
347
A
ALA
348
n
354
ALA
348
A
VAL
349
n
355
VAL
349
A
GLU
350
n
356
GLU
350
A
GLN
351
n
357
GLN
351
A
GLN
352
n
358
GLN
352
A
MET
353
n
359
MET
353
A
ASN
354
n
360
ASN
354
A
GLU
355
n
361
GLU
355
A
LEU
356
n
362
LEU
356
A
LEU
357
n
363
LEU
357
A
ALA
358
n
364
ALA
358
A
GLU
359
n
365
GLU
359
A
TYR
360
n
366
TYR
360
A
LEU
361
n
367
LEU
361
A
LEU
362
n
368
LEU
362
A
GLU
363
n
369
GLU
363
A
ASN
364
n
370
ASN
364
A
PRO
365
n
371
PRO
365
A
THR
366
n
372
THR
366
A
ASP
367
n
373
ASP
367
A
ALA
368
n
374
ALA
368
A
LYS
369
n
375
LYS
369
A
ILE
370
n
376
ILE
370
A
VAL
371
n
377
VAL
371
A
VAL
372
n
378
VAL
372
A
GLY
373
n
379
GLY
373
A
LYS
374
n
380
LYS
374
A
ILE
375
n
381
ILE
375
A
ILE
376
n
382
ILE
376
A
ASP
377
n
383
ASP
377
A
ALA
378
n
384
ALA
378
A
ALA
379
n
385
ALA
379
A
ARG
380
n
386
ARG
380
A
ALA
381
n
387
ALA
381
A
ARG
382
n
388
ARG
382
A
GLU
383
n
389
GLU
383
A
ALA
384
n
390
ALA
384
A
ALA
385
n
391
ALA
385
A
ARG
386
n
392
ARG
386
A
n
393
387
A
n
394
388
A
n
395
389
A
n
396
390
A
n
397
391
A
n
398
392
A
author_and_software_defined_assembly
PISA
2
dimeric
6400
-54
29150
A
ASN
46
A
OD1
ASN
52
1_555
A
MG
402
C
MG
MG
1_555
A
ADP
401
B
O3B
ADP
1_555
90.4
A
ASN
46
A
OD1
ASN
52
1_555
A
MG
402
C
MG
MG
1_555
A
ADP
401
B
O2A
ADP
1_555
102.9
A
ADP
401
B
O3B
ADP
1_555
A
MG
402
C
MG
MG
1_555
A
ADP
401
B
O2A
ADP
1_555
93.6
A
ASN
46
A
OD1
ASN
52
1_555
A
MG
402
C
MG
MG
1_555
A
HOH
527
D
O
HOH
1_555
90.5
A
ADP
401
B
O3B
ADP
1_555
A
MG
402
C
MG
MG
1_555
A
HOH
527
D
O
HOH
1_555
171.2
A
ADP
401
B
O2A
ADP
1_555
A
MG
402
C
MG
MG
1_555
A
HOH
527
D
O
HOH
1_555
94.8
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
3_554
-x,y,-z-1/2
crystal symmetry operation
0.0000000000
0.0000000000
-39.5450000000
A
O
VAL
149
A
O
VAL
155
A
N
GLU
146
A
N
GLU
152
A
N
ILE
140
A
N
ILE
146
A
O
THR
157
A
O
THR
163
A
O
VAL
149
A
O
VAL
155
A
N
GLU
146
A
N
GLU
152
A
O
GLN
143
A
O
GLN
149
A
N
LEU
132
A
N
LEU
138
A
N
GLU
131
A
N
GLU
137
A
O
ARG
168
A
O
ARG
174
A
O
VAL
167
A
O
VAL
173
A
N
VAL
71
A
N
VAL
77
A
O
GLN
72
A
O
GLN
78
A
N
ILE
60
A
N
ILE
66
A
N
ILE
59
A
N
ILE
65
A
O
ARG
204
A
O
ARG
210
A
N
ILE
203
A
N
ILE
209
A
O
PHE
216
A
O
PHE
222
A
N
THR
245
A
N
THR
251
A
O
VAL
252
A
O
VAL
258
A
N
ALA
255
A
N
ALA
261
A
O
VAL
322
A
O
VAL
328
A
O
VAL
323
A
O
VAL
329
A
N
TYR
267
A
N
TYR
273
A
N
THR
270
A
N
THR
276
A
O
ILE
273
A
O
ILE
279
1
A
HOH
626
D
HOH
1
A
CD
LYS
11
A
CD
LYS
17
1
Y
1
A
CE
LYS
11
A
CE
LYS
17
1
Y
1
A
NZ
LYS
11
A
NZ
LYS
17
1
Y
1
A
CD
LYS
14
A
CD
LYS
20
1
Y
1
A
CE
LYS
14
A
CE
LYS
20
1
Y
1
A
NZ
LYS
14
A
NZ
LYS
20
1
Y
1
A
CE
LYS
57
A
CE
LYS
63
1
Y
1
A
NZ
LYS
57
A
NZ
LYS
63
1
Y
1
A
CD
LYS
110
A
CD
LYS
116
1
Y
1
A
CE
LYS
110
A
CE
LYS
116
1
Y
1
A
NZ
LYS
110
A
NZ
LYS
116
1
Y
1
A
CG
LYS
139
A
CG
LYS
145
1
Y
1
A
CD
LYS
139
A
CD
LYS
145
1
Y
1
A
CE
LYS
139
A
CE
LYS
145
1
Y
1
A
NZ
LYS
139
A
NZ
LYS
145
1
Y
1
A
CG
GLU
159
A
CG
GLU
165
1
Y
1
A
CD
GLU
159
A
CD
GLU
165
1
Y
1
A
OE1
GLU
159
A
OE1
GLU
165
1
Y
1
A
OE2
GLU
159
A
OE2
GLU
165
1
Y
1
A
CG
GLU
161
A
CG
GLU
167
1
Y
1
A
CD
GLU
161
A
CD
GLU
167
1
Y
1
A
OE1
GLU
161
A
OE1
GLU
167
1
Y
1
A
OE2
GLU
161
A
OE2
GLU
167
1
Y
1
A
CD
LYS
162
A
CD
LYS
168
1
Y
1
A
CE
LYS
162
A
CE
LYS
168
1
Y
1
A
NZ
LYS
162
A
NZ
LYS
168
1
Y
1
A
CD
LYS
189
A
CD
LYS
195
1
Y
1
A
CE
LYS
189
A
CE
LYS
195
1
Y
1
A
NZ
LYS
189
A
NZ
LYS
195
1
Y
1
A
CG
LYS
212
A
CG
LYS
218
1
Y
1
A
CD
LYS
212
A
CD
LYS
218
1
Y
1
A
CE
LYS
212
A
CE
LYS
218
1
Y
1
A
NZ
LYS
212
A
NZ
LYS
218
1
Y
1
A
CG
ARG
382
A
CG
ARG
388
1
Y
1
A
CD
ARG
382
A
CD
ARG
388
1
Y
1
A
NE
ARG
382
A
NE
ARG
388
1
Y
1
A
CZ
ARG
382
A
CZ
ARG
388
1
Y
1
A
NH1
ARG
382
A
NH1
ARG
388
1
Y
1
A
NH2
ARG
382
A
NH2
ARG
388
1
Y
1
A
CB
ARG
386
A
CB
ARG
392
1
Y
1
A
CG
ARG
386
A
CG
ARG
392
1
Y
1
A
CD
ARG
386
A
CD
ARG
392
1
Y
1
A
NE
ARG
386
A
NE
ARG
392
1
Y
1
A
CZ
ARG
386
A
CZ
ARG
392
1
Y
1
A
NH1
ARG
386
A
NH1
ARG
392
1
Y
1
A
NH2
ARG
386
A
NH2
ARG
392
1
Y
1
A
MET
-5
A
MET
1
1
Y
1
A
HIS
-4
A
HIS
2
1
Y
1
A
HIS
-3
A
HIS
3
1
Y
1
A
HIS
-2
A
HIS
4
1
Y
1
A
HIS
-1
A
HIS
5
1
Y
1
A
HIS
0
A
HIS
6
1
Y
1
A
HIS
1
A
HIS
7
1
Y
1
A
SER
2
A
SER
8
1
Y
1
A
ASN
3
A
ASN
9
1
Y
1
A
SER
4
A
SER
10
1
Y
1
A
SER
303
A
SER
309
1
Y
1
A
LYS
304
A
LYS
310
1
Y
1
A
LYS
305
A
LYS
311
1
Y
1
A
ALA
306
A
ALA
312
1
Y
1
A
LYS
307
A
LYS
313
1
Y
1
A
VAL
308
A
VAL
314
1
Y
1
A
SER
309
A
SER
315
1
Y
1
A
ALA
310
A
ALA
316
1
Y
1
A
THR
311
A
THR
317
1
Y
1
A
GLY
312
A
GLY
318
1
Y
1
A
ASP
313
A
ASP
319
1
Y
1
A
ASP
314
A
ASP
320
1
Y
1
A
ALA
315
A
ALA
321
1
Y
1
A
ARG
387
A
ARG
393
1
Y
1
A
ALA
388
A
ALA
394
1
Y
1
A
ARG
389
A
ARG
395
1
Y
1
A
GLU
390
A
GLU
396
1
Y
1
A
MET
391
A
MET
397
1
Y
1
A
THR
392
A
THR
398
1
Y
1
3.04
0.50
120.30
123.34
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
276
276
276
B
B
B
N
1
3.24
0.50
120.30
123.54
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
316
316
316
N
1
A
ASP
6
-161.23
-162.35
1
A
ASP
74
-103.62
40.66
1
A
LEU
115
-175.19
-24.66
1
A
ASN
178
70.41
-74.52
1
A
HIS
217
-153.46
49.42
1
A
ASN
272
76.57
-3.07
1
A
LYS
337
71.47
35.86
89.400
28.9520
13.720
-1.4200
-0.0000
0.0000
1.9700
0.0000
-0.5500
0.9370
0.8930
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
0.2587
0.2067
0.2102
2.0000
75.0300
2011
30052
30052
6.7000
88.2200
0.2265
0.1778
0.7899
4.3840
0.1190
0.1913
0.1808
RANDOM
1
THROUGHOUT
0.000
-3.000
MOLECULAR REPLACEMENT
0.1810
0.8000
0.8000
1.2000
1EI1
MAXIMUM LIKELIHOOD
MASK
2.0000
75.0300
126
2982
28
0
2828
0.018
0.019
2940
0.001
0.020
2746
1.883
1.958
3993
0.915
3.000
6306
6.290
5.000
373
39.496
24.526
137
15.165
15.000
481
19.323
15.000
17
0.120
0.200
447
0.009
0.020
3385
0.001
0.020
673
0.3330
0.2870
2.0520
164
2261
2425
20
97.3900
32.303
2.000
75.030
4PRV
30053
30053
0
-3.000
0.068
0.951
1
22.150
88.200
0.935
0.583
2.000
2.120
3.320
29579
5380
5155
0.644
1
0
95.800
0.947
0.365
2.120
2.270
5.240
24254
5267
3722
0.396
1
0
70.700
0.981
0.215
2.270
2.450
9.040
29817
4717
4396
0.232
1
0
93.200
0.990
0.153
2.450
2.680
12.540
24990
4338
3715
0.165
1
0
85.600
0.996
0.085
2.680
3.000
20.230
22830
4045
3673
0.092
1
0
90.800
0.999
0.049
3.000
3.460
33.390
21561
3533
3242
0.054
1
0
91.800
0.999
0.031
3.460
4.240
50.000
15759
3033
2394
0.034
1
0
78.900
1.000
0.024
4.240
5.980
59.770
14856
2378
2375
0.026
1
0
99.900
0.999
0.019
5.980
75.030
71.350
9082
1382
1381
0.021
1
0
99.900
data scaling
Wolfgang Kabsch
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html
XSCALE
package
phasing
Randy J. Read
cimr-phaser@lists.cam.ac.uk
Fri Oct 21 16:31:14 2011 (svn )
http://www-structmed.cimr.cam.ac.uk/phaser/
PHASER
program
2.3.0
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
5.7.0029
data extraction
PDB
deposit@deposit.rcsb.org
Dec. 10, 2013
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.14
data reduction
XDS
E. coli GyrB 43-kDa N-terminal fragment in complex with ADP
1
N
N
2
N
N
3
N
N
4
N
N
A
ASP
6
A
ASP
12
HELX_P
A
ILE
10
A
ILE
16
5
1
5
A
LEU
16
A
LEU
22
HELX_P
A
ARG
22
A
ARG
28
1
2
7
A
PRO
23
A
PRO
29
HELX_P
A
GLY
28
A
GLY
34
1
3
6
A
GLY
33
A
GLY
39
HELX_P
A
ALA
53
A
ALA
59
1
4
21
A
SER
89
A
SER
95
HELX_P
A
VAL
97
A
VAL
103
1
5
9
A
VAL
118
A
VAL
124
HELX_P
A
LEU
126
A
LEU
132
1
6
9
A
GLU
183
A
GLU
189
HELX_P
A
ASN
198
A
ASN
204
1
7
16
A
GLY
220
A
GLY
226
HELX_P
A
LYS
231
A
LYS
237
1
8
12
A
GLY
279
A
GLY
285
HELX_P
A
GLU
300
A
GLU
306
1
9
22
A
SER
342
A
SER
348
HELX_P
A
ASN
364
A
ASN
370
1
10
23
A
ASN
364
A
ASN
370
HELX_P
A
ARG
386
A
ARG
392
1
11
23
metalc
2.204
A
ASN
46
A
OD1
ASN
52
1_555
A
MG
402
C
MG
MG
1_555
metalc
2.226
A
ADP
401
B
O3B
ADP
1_555
A
MG
402
C
MG
MG
1_555
metalc
2.294
A
ADP
401
B
O2A
ADP
1_555
A
MG
402
C
MG
MG
1_555
metalc
2.319
A
MG
402
C
MG
MG
1_555
A
HOH
527
D
O
HOH
1_555
ISOMERASE
GyrB, ATP hydrolysis, ISOMERASE
GYRB_ECOLI
UNP
1
2
P0AES6
SNSYDSSSIKVLKGLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHADNSVSVQDDGRGIPTG
IHPEEGVSAAEVIMTVLHAGGKFDDNSYKVSGGLHGVGVSVVNALSQKLELVIQREGKIHRQIYEHGVPQAPLAVTGETE
KTGTMVRFWPSLETFTNVTEFEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTPIHPNIF
YFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIA
VVSVKVPDPKFSSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAARRAREMT
2
392
4PRV
2
392
P0AES6
A
1
8
398
1
expression tag
MET
-5
4PRV
A
P0AES6
UNP
1
1
expression tag
HIS
-4
4PRV
A
P0AES6
UNP
2
1
expression tag
HIS
-3
4PRV
A
P0AES6
UNP
3
1
expression tag
HIS
-2
4PRV
A
P0AES6
UNP
4
1
expression tag
HIS
-1
4PRV
A
P0AES6
UNP
5
1
expression tag
HIS
0
4PRV
A
P0AES6
UNP
6
1
expression tag
HIS
1
4PRV
A
P0AES6
UNP
7
3
8
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
A
VAL
149
A
VAL
155
A
PRO
150
A
PRO
156
A
LYS
139
A
LYS
145
A
GLU
146
A
GLU
152
A
ALA
155
A
ALA
161
A
GLU
159
A
GLU
165
A
VAL
149
A
VAL
155
A
PRO
150
A
PRO
156
A
LYS
139
A
LYS
145
A
GLU
146
A
GLU
152
A
SER
127
A
SER
133
A
ARG
136
A
ARG
142
A
GLY
164
A
GLY
170
A
PRO
171
A
PRO
177
A
VAL
69
A
VAL
75
A
ASP
73
A
ASP
79
A
GLU
58
A
GLU
64
A
ILE
63
A
ILE
69
A
SER
202
A
SER
208
A
ASP
207
A
ASP
213
A
GLU
213
A
GLU
219
A
PHE
216
A
PHE
222
A
PHE
241
A
PHE
247
A
LYS
247
A
LYS
253
A
ILE
250
A
ILE
256
A
TRP
258
A
TRP
264
A
LEU
319
A
LEU
325
A
LYS
326
A
LYS
332
A
ASN
265
A
ASN
271
A
THR
270
A
THR
276
A
ILE
273
A
ILE
279
A
PRO
274
A
PRO
280
BINDING SITE FOR RESIDUE ADP A 401
A
ADP
401
Software
27
BINDING SITE FOR RESIDUE MG A 402
A
MG
402
Software
3
A
TYR
5
A
TYR
11
27
3_554
A
ILE
10
A
ILE
16
27
3_554
A
ASN
46
A
ASN
52
27
1_555
A
GLU
50
A
GLU
56
27
1_555
A
ASP
73
A
ASP
79
27
1_555
A
ILE
78
A
ILE
84
27
1_555
A
ILE
94
A
ILE
100
27
1_555
A
ALA
100
A
ALA
106
27
1_555
A
GLY
101
A
GLY
107
27
1_555
A
GLY
102
A
GLY
108
27
1_555
A
LYS
103
A
LYS
109
27
1_555
A
TYR
109
A
TYR
115
27
1_555
A
GLY
114
A
GLY
120
27
1_555
A
LEU
115
A
LEU
121
27
1_555
A
HIS
116
A
HIS
122
27
1_555
A
GLY
117
A
GLY
123
27
1_555
A
VAL
118
A
VAL
124
27
1_555
A
GLY
119
A
GLY
125
27
1_555
A
VAL
120
A
VAL
126
27
1_555
A
THR
165
A
THR
171
27
1_555
A
MG
402
C
MG
27
1_555
A
HOH
533
D
HOH
27
1_555
A
HOH
534
D
HOH
27
1_555
A
HOH
541
D
HOH
27
1_555
A
HOH
551
D
HOH
27
1_555
A
HOH
574
D
HOH
27
1_555
A
HOH
625
D
HOH
27
1_555
A
ASN
46
A
ASN
52
3
1_555
A
ADP
401
B
ADP
3
1_555
A
HOH
527
D
HOH
3
1_555
20
C 2 2 21