0.012180
0.000000
0.002470
0.000000
0.026700
0.000000
0.000000
0.000000
0.014650
0.00000
0.00000
0.00000
Chruszcz, M.
Xu, X.
Cuff, M.
Cymborowski, M.
Zheng, H.
Savchenko, A.
Edwards, A.
Joachimiak, A.
0000-0001-7075-7090
Minor, W.
Midwest Center for Structural Genomics (MCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
101.48
90.00
82.095
37.454
69.636
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
Cl -1
35.453
CHLORIDE ION
non-polymer
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
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
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
UK
Febs J.
1742-464X
279
1093
1105
10.1111/j.1742-4658.2012.08506.x
22284390
Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members.
2012
0000-0001-7075-7090
10.2210/pdb2qmo/pdb
pdb_00002qmo
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
MIRROR
CCD
2007-04-15
ADSC QUANTUM 315
SI-111 CHANNEL
SINGLE WAVELENGTH
M
x-ray
1
0.97918
1.0
19-ID
APS
0.97918
SYNCHROTRON
APS BEAMLINE 19-ID
24817.002
Dethiobiotin synthetase
6.3.3.3
1
man
polymer
35.453
CHLORIDE ION
2
syn
non-polymer
18.015
water
326
nat
water
Dethiobiotin synthase, DTB synthetase, DTBS
no
yes
GH(MSE)LFISATNTNAGKTTCARLLAQYCNACGVKTILLKPIETGVNDAINHSSDAHLFLQDNRLLDRSLTLKDISFYR
YHKVSAPLIAQQEEDPNAPIDTDNLTQRLHNFTKTYDLVIVEGAGGLCVPITLEEN(MSE)LDFALKLKAK(MSE)LLIS
HDNLGLINDCLLNDFLLKSHQLDYKIAINLKGNNTAFHSISLPYIELFNTRSNNPIVIFQQSLKVL(MSE)SFALK
GHMLFISATNTNAGKTTCARLLAQYCNACGVKTILLKPIETGVNDAINHSSDAHLFLQDNRLLDRSLTLKDISFYRYHKV
SAPLIAQQEEDPNAPIDTDNLTQRLHNFTKTYDLVIVEGAGGLCVPITLEENMLDFALKLKAKMLLISHDNLGLINDCLL
NDFLLKSHQLDYKIAINLKGNNTAFHSISLPYIELFNTRSNNPIVIFQQSLKVLMSFALK
A
APC5858
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
Helicobacter
Helicobacter pylori
26695
Escherichia
sample
700392
bioD, HP_0029
85962
Helicobacter pylori
562
Escherichia coli
BL21-Gold (DE3)
Plasmid
p11
1
2.11
41.81
VAPOR DIFFUSION
VAPOR DIFFUSION, temperature 273K
273
Midwest Center for Structural Genomics
MCSG
PSI, Protein Structure Initiative
audit_author
citation_author
database_2
pdbx_struct_special_symmetry
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Advisory
Source and taxonomy
Version format compliance
Database references
Database references
Database references
Derived calculations
Structure summary
1
0
2007-07-31
1
1
2011-07-13
1
2
2012-03-28
1
3
2013-03-27
1
4
2022-04-13
_audit_author.identifier_ORCID
_citation_author.identifier_ORCID
_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
2007-07-16
REL
REL
CL
CHLORIDE ION
HOH
water
CL
1
2
CL
CL
301
A
CL
1
2
CL
CL
302
A
HOH
2
3
HOH
HOH
303
A
HOH
2
3
HOH
HOH
304
A
HOH
3
3
HOH
HOH
305
A
HOH
3
3
HOH
HOH
306
A
HOH
4
3
HOH
HOH
307
A
HOH
4
3
HOH
HOH
308
A
HOH
5
3
HOH
HOH
309
A
HOH
5
3
HOH
HOH
310
A
HOH
6
3
HOH
HOH
311
A
HOH
6
3
HOH
HOH
312
A
HOH
7
3
HOH
HOH
313
A
HOH
8
3
HOH
HOH
314
A
HOH
8
3
HOH
HOH
315
A
HOH
9
3
HOH
HOH
316
A
HOH
9
3
HOH
HOH
317
A
HOH
10
3
HOH
HOH
318
A
HOH
10
3
HOH
HOH
319
A
HOH
12
3
HOH
HOH
320
A
HOH
12
3
HOH
HOH
321
A
HOH
13
3
HOH
HOH
322
A
HOH
13
3
HOH
HOH
323
A
HOH
15
3
HOH
HOH
324
A
HOH
15
3
HOH
HOH
325
A
HOH
16
3
HOH
HOH
326
A
HOH
16
3
HOH
HOH
327
A
HOH
17
3
HOH
HOH
328
A
HOH
18
3
HOH
HOH
329
A
HOH
18
3
HOH
HOH
330
A
HOH
19
3
HOH
HOH
331
A
HOH
19
3
HOH
HOH
332
A
HOH
20
3
HOH
HOH
333
A
HOH
21
3
HOH
HOH
334
A
HOH
21
3
HOH
HOH
335
A
HOH
23
3
HOH
HOH
336
A
HOH
23
3
HOH
HOH
337
A
HOH
24
3
HOH
HOH
338
A
HOH
24
3
HOH
HOH
339
A
HOH
25
3
HOH
HOH
340
A
HOH
25
3
HOH
HOH
341
A
HOH
26
3
HOH
HOH
342
A
HOH
26
3
HOH
HOH
343
A
HOH
27
3
HOH
HOH
344
A
HOH
27
3
HOH
HOH
345
A
HOH
28
3
HOH
HOH
346
A
HOH
28
3
HOH
HOH
347
A
HOH
30
3
HOH
HOH
348
A
HOH
30
3
HOH
HOH
349
A
HOH
31
3
HOH
HOH
350
A
HOH
31
3
HOH
HOH
351
A
HOH
32
3
HOH
HOH
352
A
HOH
32
3
HOH
HOH
353
A
HOH
33
3
HOH
HOH
354
A
HOH
33
3
HOH
HOH
355
A
HOH
34
3
HOH
HOH
356
A
HOH
34
3
HOH
HOH
357
A
HOH
35
3
HOH
HOH
358
A
HOH
35
3
HOH
HOH
359
A
HOH
36
3
HOH
HOH
360
A
HOH
36
3
HOH
HOH
361
A
HOH
37
3
HOH
HOH
362
A
HOH
37
3
HOH
HOH
363
A
HOH
38
3
HOH
HOH
364
A
HOH
38
3
HOH
HOH
365
A
HOH
39
3
HOH
HOH
366
A
HOH
40
3
HOH
HOH
367
A
HOH
41
3
HOH
HOH
368
A
HOH
41
3
HOH
HOH
369
A
HOH
42
3
HOH
HOH
370
A
HOH
42
3
HOH
HOH
371
A
HOH
43
3
HOH
HOH
372
A
HOH
43
3
HOH
HOH
373
A
HOH
44
3
HOH
HOH
374
A
HOH
44
3
HOH
HOH
375
A
HOH
45
3
HOH
HOH
376
A
HOH
45
3
HOH
HOH
377
A
HOH
47
3
HOH
HOH
378
A
HOH
47
3
HOH
HOH
379
A
HOH
48
3
HOH
HOH
380
A
HOH
48
3
HOH
HOH
381
A
HOH
49
3
HOH
HOH
382
A
HOH
49
3
HOH
HOH
383
A
HOH
50
3
HOH
HOH
384
A
HOH
51
3
HOH
HOH
385
A
HOH
52
3
HOH
HOH
386
A
HOH
53
3
HOH
HOH
387
A
HOH
54
3
HOH
HOH
388
A
HOH
55
3
HOH
HOH
389
A
HOH
56
3
HOH
HOH
390
A
HOH
57
3
HOH
HOH
391
A
HOH
58
3
HOH
HOH
392
A
HOH
60
3
HOH
HOH
393
A
HOH
61
3
HOH
HOH
394
A
HOH
62
3
HOH
HOH
395
A
HOH
63
3
HOH
HOH
396
A
HOH
64
3
HOH
HOH
397
A
HOH
65
3
HOH
HOH
398
A
HOH
66
3
HOH
HOH
399
A
HOH
67
3
HOH
HOH
400
A
HOH
68
3
HOH
HOH
401
A
HOH
69
3
HOH
HOH
402
A
HOH
70
3
HOH
HOH
403
A
HOH
71
3
HOH
HOH
404
A
HOH
72
3
HOH
HOH
405
A
HOH
73
3
HOH
HOH
406
A
HOH
74
3
HOH
HOH
407
A
HOH
75
3
HOH
HOH
408
A
HOH
76
3
HOH
HOH
409
A
HOH
77
3
HOH
HOH
410
A
HOH
78
3
HOH
HOH
411
A
HOH
79
3
HOH
HOH
412
A
HOH
81
3
HOH
HOH
413
A
HOH
83
3
HOH
HOH
414
A
HOH
85
3
HOH
HOH
415
A
HOH
86
3
HOH
HOH
416
A
HOH
87
3
HOH
HOH
417
A
HOH
88
3
HOH
HOH
418
A
HOH
89
3
HOH
HOH
419
A
HOH
90
3
HOH
HOH
420
A
HOH
91
3
HOH
HOH
421
A
HOH
92
3
HOH
HOH
422
A
HOH
93
3
HOH
HOH
423
A
HOH
94
3
HOH
HOH
424
A
HOH
95
3
HOH
HOH
425
A
HOH
96
3
HOH
HOH
426
A
HOH
97
3
HOH
HOH
427
A
HOH
98
3
HOH
HOH
428
A
HOH
99
3
HOH
HOH
429
A
HOH
100
3
HOH
HOH
430
A
HOH
101
3
HOH
HOH
431
A
HOH
102
3
HOH
HOH
432
A
HOH
103
3
HOH
HOH
433
A
HOH
104
3
HOH
HOH
434
A
HOH
105
3
HOH
HOH
435
A
HOH
106
3
HOH
HOH
436
A
HOH
107
3
HOH
HOH
437
A
HOH
108
3
HOH
HOH
438
A
HOH
109
3
HOH
HOH
439
A
HOH
110
3
HOH
HOH
440
A
HOH
111
3
HOH
HOH
441
A
HOH
112
3
HOH
HOH
442
A
HOH
113
3
HOH
HOH
443
A
HOH
114
3
HOH
HOH
444
A
HOH
116
3
HOH
HOH
445
A
HOH
118
3
HOH
HOH
446
A
HOH
119
3
HOH
HOH
447
A
HOH
120
3
HOH
HOH
448
A
HOH
121
3
HOH
HOH
449
A
HOH
122
3
HOH
HOH
450
A
HOH
124
3
HOH
HOH
451
A
HOH
125
3
HOH
HOH
452
A
HOH
126
3
HOH
HOH
453
A
HOH
127
3
HOH
HOH
454
A
HOH
128
3
HOH
HOH
455
A
HOH
129
3
HOH
HOH
456
A
HOH
130
3
HOH
HOH
457
A
HOH
131
3
HOH
HOH
458
A
HOH
132
3
HOH
HOH
459
A
HOH
133
3
HOH
HOH
460
A
HOH
134
3
HOH
HOH
461
A
HOH
135
3
HOH
HOH
462
A
HOH
137
3
HOH
HOH
463
A
HOH
138
3
HOH
HOH
464
A
HOH
139
3
HOH
HOH
465
A
HOH
140
3
HOH
HOH
466
A
HOH
141
3
HOH
HOH
467
A
HOH
142
3
HOH
HOH
468
A
HOH
143
3
HOH
HOH
469
A
HOH
144
3
HOH
HOH
470
A
HOH
145
3
HOH
HOH
471
A
HOH
146
3
HOH
HOH
472
A
HOH
147
3
HOH
HOH
473
A
HOH
148
3
HOH
HOH
474
A
HOH
150
3
HOH
HOH
475
A
HOH
151
3
HOH
HOH
476
A
HOH
152
3
HOH
HOH
477
A
HOH
153
3
HOH
HOH
478
A
HOH
154
3
HOH
HOH
479
A
HOH
155
3
HOH
HOH
480
A
HOH
157
3
HOH
HOH
481
A
HOH
158
3
HOH
HOH
482
A
HOH
159
3
HOH
HOH
483
A
HOH
160
3
HOH
HOH
484
A
HOH
161
3
HOH
HOH
485
A
HOH
163
3
HOH
HOH
486
A
HOH
164
3
HOH
HOH
487
A
HOH
165
3
HOH
HOH
488
A
HOH
166
3
HOH
HOH
489
A
HOH
167
3
HOH
HOH
490
A
HOH
168
3
HOH
HOH
491
A
HOH
169
3
HOH
HOH
492
A
HOH
170
3
HOH
HOH
493
A
HOH
171
3
HOH
HOH
494
A
HOH
172
3
HOH
HOH
495
A
HOH
173
3
HOH
HOH
496
A
HOH
175
3
HOH
HOH
497
A
HOH
178
3
HOH
HOH
498
A
HOH
179
3
HOH
HOH
499
A
HOH
180
3
HOH
HOH
500
A
HOH
182
3
HOH
HOH
501
A
HOH
183
3
HOH
HOH
502
A
HOH
184
3
HOH
HOH
503
A
HOH
187
3
HOH
HOH
504
A
HOH
189
3
HOH
HOH
505
A
HOH
190
3
HOH
HOH
506
A
HOH
191
3
HOH
HOH
507
A
HOH
192
3
HOH
HOH
508
A
HOH
193
3
HOH
HOH
509
A
HOH
194
3
HOH
HOH
510
A
HOH
195
3
HOH
HOH
511
A
HOH
196
3
HOH
HOH
512
A
HOH
198
3
HOH
HOH
513
A
HOH
199
3
HOH
HOH
514
A
HOH
200
3
HOH
HOH
515
A
HOH
201
3
HOH
HOH
516
A
HOH
202
3
HOH
HOH
517
A
HOH
203
3
HOH
HOH
518
A
HOH
204
3
HOH
HOH
519
A
HOH
206
3
HOH
HOH
520
A
HOH
207
3
HOH
HOH
521
A
HOH
208
3
HOH
HOH
522
A
HOH
210
3
HOH
HOH
523
A
HOH
211
3
HOH
HOH
524
A
HOH
212
3
HOH
HOH
525
A
HOH
213
3
HOH
HOH
526
A
HOH
214
3
HOH
HOH
527
A
HOH
215
3
HOH
HOH
528
A
HOH
216
3
HOH
HOH
529
A
HOH
217
3
HOH
HOH
530
A
HOH
218
3
HOH
HOH
531
A
HOH
219
3
HOH
HOH
532
A
HOH
220
3
HOH
HOH
533
A
HOH
221
3
HOH
HOH
534
A
HOH
222
3
HOH
HOH
535
A
HOH
223
3
HOH
HOH
536
A
HOH
224
3
HOH
HOH
537
A
HOH
225
3
HOH
HOH
538
A
HOH
226
3
HOH
HOH
539
A
HOH
227
3
HOH
HOH
540
A
HOH
228
3
HOH
HOH
541
A
HOH
229
3
HOH
HOH
542
A
HOH
230
3
HOH
HOH
543
A
HOH
231
3
HOH
HOH
544
A
HOH
232
3
HOH
HOH
545
A
HOH
233
3
HOH
HOH
546
A
HOH
234
3
HOH
HOH
547
A
HOH
235
3
HOH
HOH
548
A
HOH
236
3
HOH
HOH
549
A
HOH
237
3
HOH
HOH
550
A
HOH
238
3
HOH
HOH
551
A
HOH
239
3
HOH
HOH
552
A
HOH
240
3
HOH
HOH
553
A
HOH
241
3
HOH
HOH
554
A
HOH
242
3
HOH
HOH
555
A
HOH
243
3
HOH
HOH
556
A
HOH
244
3
HOH
HOH
557
A
HOH
245
3
HOH
HOH
558
A
HOH
246
3
HOH
HOH
559
A
HOH
247
3
HOH
HOH
560
A
HOH
248
3
HOH
HOH
561
A
HOH
249
3
HOH
HOH
562
A
HOH
250
3
HOH
HOH
563
A
HOH
251
3
HOH
HOH
564
A
HOH
253
3
HOH
HOH
565
A
HOH
254
3
HOH
HOH
566
A
HOH
256
3
HOH
HOH
567
A
HOH
257
3
HOH
HOH
568
A
HOH
258
3
HOH
HOH
569
A
HOH
259
3
HOH
HOH
570
A
HOH
260
3
HOH
HOH
571
A
HOH
261
3
HOH
HOH
572
A
HOH
262
3
HOH
HOH
573
A
HOH
263
3
HOH
HOH
574
A
HOH
264
3
HOH
HOH
575
A
HOH
265
3
HOH
HOH
576
A
HOH
266
3
HOH
HOH
577
A
HOH
267
3
HOH
HOH
578
A
HOH
268
3
HOH
HOH
579
A
HOH
269
3
HOH
HOH
580
A
HOH
270
3
HOH
HOH
581
A
HOH
271
3
HOH
HOH
582
A
HOH
272
3
HOH
HOH
583
A
HOH
273
3
HOH
HOH
584
A
HOH
274
3
HOH
HOH
585
A
HOH
275
3
HOH
HOH
586
A
HOH
276
3
HOH
HOH
587
A
HOH
277
3
HOH
HOH
588
A
HOH
278
3
HOH
HOH
589
A
HOH
280
3
HOH
HOH
590
A
HOH
281
3
HOH
HOH
591
A
HOH
282
3
HOH
HOH
592
A
HOH
283
3
HOH
HOH
593
A
HOH
284
3
HOH
HOH
594
A
HOH
285
3
HOH
HOH
595
A
HOH
286
3
HOH
HOH
596
A
HOH
287
3
HOH
HOH
597
A
HOH
288
3
HOH
HOH
598
A
HOH
289
3
HOH
HOH
599
A
HOH
290
3
HOH
HOH
600
A
HOH
291
3
HOH
HOH
601
A
HOH
292
3
HOH
HOH
602
A
HOH
293
3
HOH
HOH
603
A
HOH
294
3
HOH
HOH
604
A
HOH
295
3
HOH
HOH
605
A
HOH
296
3
HOH
HOH
606
A
HOH
297
3
HOH
HOH
607
A
HOH
298
3
HOH
HOH
608
A
HOH
299
3
HOH
HOH
609
A
HOH
300
3
HOH
HOH
610
A
HOH
301
3
HOH
HOH
611
A
HOH
302
3
HOH
HOH
612
A
HOH
304
3
HOH
HOH
613
A
HOH
305
3
HOH
HOH
614
A
HOH
306
3
HOH
HOH
615
A
HOH
307
3
HOH
HOH
616
A
HOH
308
3
HOH
HOH
617
A
HOH
309
3
HOH
HOH
618
A
HOH
310
3
HOH
HOH
619
A
HOH
312
3
HOH
HOH
620
A
HOH
313
3
HOH
HOH
621
A
HOH
315
3
HOH
HOH
622
A
HOH
316
3
HOH
HOH
623
A
HOH
1
3
HOH
HOH
624
A
HOH
11
3
HOH
HOH
625
A
HOH
14
3
HOH
HOH
626
A
HOH
22
3
HOH
HOH
627
A
HOH
29
3
HOH
HOH
628
A
GLY
-1
n
1
GLY
-1
A
HIS
0
n
2
HIS
0
A
MSE
1
n
3
MSE
1
A
LEU
2
n
4
LEU
2
A
PHE
3
n
5
PHE
3
A
ILE
4
n
6
ILE
4
A
SER
5
n
7
SER
5
A
ALA
6
n
8
ALA
6
A
THR
7
n
9
THR
7
A
ASN
8
n
10
ASN
8
A
THR
9
n
11
THR
9
A
ASN
10
n
12
ASN
10
A
ALA
11
n
13
ALA
11
A
GLY
12
n
14
GLY
12
A
LYS
13
n
15
LYS
13
A
THR
14
n
16
THR
14
A
THR
15
n
17
THR
15
A
CYS
16
n
18
CYS
16
A
ALA
17
n
19
ALA
17
A
ARG
18
n
20
ARG
18
A
LEU
19
n
21
LEU
19
A
LEU
20
n
22
LEU
20
A
ALA
21
n
23
ALA
21
A
GLN
22
n
24
GLN
22
A
TYR
23
n
25
TYR
23
A
CYS
24
n
26
CYS
24
A
ASN
25
n
27
ASN
25
A
ALA
26
n
28
ALA
26
A
CYS
27
n
29
CYS
27
A
GLY
28
n
30
GLY
28
A
VAL
29
n
31
VAL
29
A
LYS
30
n
32
LYS
30
A
THR
31
n
33
THR
31
A
ILE
32
n
34
ILE
32
A
LEU
33
n
35
LEU
33
A
LEU
34
n
36
LEU
34
A
LYS
35
n
37
LYS
35
A
PRO
36
n
38
PRO
36
A
ILE
37
n
39
ILE
37
A
GLU
38
n
40
GLU
38
A
THR
39
n
41
THR
39
A
GLY
40
n
42
GLY
40
A
VAL
41
n
43
VAL
41
A
ASN
42
n
44
ASN
42
A
ASP
43
n
45
ASP
43
A
ALA
44
n
46
ALA
44
A
ILE
45
n
47
ILE
45
A
ASN
46
n
48
ASN
46
A
HIS
47
n
49
HIS
47
A
SER
48
n
50
SER
48
A
SER
49
n
51
SER
49
A
ASP
50
n
52
ASP
50
A
ALA
51
n
53
ALA
51
A
HIS
52
n
54
HIS
52
A
LEU
53
n
55
LEU
53
A
PHE
54
n
56
PHE
54
A
LEU
55
n
57
LEU
55
A
GLN
56
n
58
GLN
56
A
ASP
57
n
59
ASP
57
A
ASN
58
n
60
ASN
58
A
ARG
59
n
61
ARG
59
A
LEU
60
n
62
LEU
60
A
LEU
61
n
63
LEU
61
A
ASP
62
n
64
ASP
62
A
ARG
63
n
65
ARG
63
A
SER
64
n
66
SER
64
A
LEU
65
n
67
LEU
65
A
THR
66
n
68
THR
66
A
LEU
67
n
69
LEU
67
A
LYS
68
n
70
LYS
68
A
ASP
69
n
71
ASP
69
A
ILE
70
n
72
ILE
70
A
SER
71
n
73
SER
71
A
PHE
72
n
74
PHE
72
A
TYR
73
n
75
TYR
73
A
ARG
74
n
76
ARG
74
A
TYR
75
n
77
TYR
75
A
HIS
76
n
78
HIS
76
A
LYS
77
n
79
LYS
77
A
VAL
78
n
80
VAL
78
A
SER
79
n
81
SER
79
A
ALA
80
n
82
ALA
80
A
PRO
81
n
83
PRO
81
A
LEU
82
n
84
LEU
82
A
ILE
83
n
85
ILE
83
A
ALA
84
n
86
ALA
84
A
GLN
85
n
87
GLN
85
A
GLN
86
n
88
GLN
86
A
GLU
87
n
89
GLU
87
A
GLU
88
n
90
GLU
88
A
ASP
89
n
91
ASP
89
A
PRO
90
n
92
PRO
90
A
ASN
91
n
93
ASN
91
A
ALA
92
n
94
ALA
92
A
PRO
93
n
95
PRO
93
A
ILE
94
n
96
ILE
94
A
ASP
95
n
97
ASP
95
A
THR
96
n
98
THR
96
A
ASP
97
n
99
ASP
97
A
ASN
98
n
100
ASN
98
A
LEU
99
n
101
LEU
99
A
THR
100
n
102
THR
100
A
GLN
101
n
103
GLN
101
A
ARG
102
n
104
ARG
102
A
LEU
103
n
105
LEU
103
A
HIS
104
n
106
HIS
104
A
ASN
105
n
107
ASN
105
A
PHE
106
n
108
PHE
106
A
THR
107
n
109
THR
107
A
LYS
108
n
110
LYS
108
A
THR
109
n
111
THR
109
A
TYR
110
n
112
TYR
110
A
ASP
111
n
113
ASP
111
A
LEU
112
n
114
LEU
112
A
VAL
113
n
115
VAL
113
A
ILE
114
n
116
ILE
114
A
VAL
115
n
117
VAL
115
A
GLU
116
n
118
GLU
116
A
GLY
117
n
119
GLY
117
A
ALA
118
n
120
ALA
118
A
GLY
119
n
121
GLY
119
A
GLY
120
n
122
GLY
120
A
LEU
121
n
123
LEU
121
A
CYS
122
n
124
CYS
122
A
VAL
123
n
125
VAL
123
A
PRO
124
n
126
PRO
124
A
ILE
125
n
127
ILE
125
A
THR
126
n
128
THR
126
A
LEU
127
n
129
LEU
127
A
GLU
128
n
130
GLU
128
A
GLU
129
n
131
GLU
129
A
ASN
130
n
132
ASN
130
A
MSE
131
n
133
MSE
131
A
LEU
132
n
134
LEU
132
A
ASP
133
n
135
ASP
133
A
PHE
134
n
136
PHE
134
A
ALA
135
n
137
ALA
135
A
LEU
136
n
138
LEU
136
A
LYS
137
n
139
LYS
137
A
LEU
138
n
140
LEU
138
A
LYS
139
n
141
LYS
139
A
ALA
140
n
142
ALA
140
A
LYS
141
n
143
LYS
141
A
MSE
142
n
144
MSE
142
A
LEU
143
n
145
LEU
143
A
LEU
144
n
146
LEU
144
A
ILE
145
n
147
ILE
145
A
SER
146
n
148
SER
146
A
HIS
147
n
149
HIS
147
A
ASP
148
n
150
ASP
148
A
ASN
149
n
151
ASN
149
A
LEU
150
n
152
LEU
150
A
GLY
151
n
153
GLY
151
A
LEU
152
n
154
LEU
152
A
ILE
153
n
155
ILE
153
A
ASN
154
n
156
ASN
154
A
ASP
155
n
157
ASP
155
A
CYS
156
n
158
CYS
156
A
LEU
157
n
159
LEU
157
A
LEU
158
n
160
LEU
158
A
ASN
159
n
161
ASN
159
A
ASP
160
n
162
ASP
160
A
PHE
161
n
163
PHE
161
A
LEU
162
n
164
LEU
162
A
LEU
163
n
165
LEU
163
A
LYS
164
n
166
LYS
164
A
SER
165
n
167
SER
165
A
HIS
166
n
168
HIS
166
A
GLN
167
n
169
GLN
167
A
LEU
168
n
170
LEU
168
A
ASP
169
n
171
ASP
169
A
TYR
170
n
172
TYR
170
A
LYS
171
n
173
LYS
171
A
ILE
172
n
174
ILE
172
A
ALA
173
n
175
ALA
173
A
ILE
174
n
176
ILE
174
A
ASN
175
n
177
ASN
175
A
LEU
176
n
178
LEU
176
A
LYS
177
n
179
LYS
177
A
GLY
178
n
180
GLY
178
A
ASN
179
n
181
ASN
179
A
ASN
180
n
182
ASN
180
A
THR
181
n
183
THR
181
A
ALA
182
n
184
ALA
182
A
PHE
183
n
185
PHE
183
A
HIS
184
n
186
HIS
184
A
SER
185
n
187
SER
185
A
ILE
186
n
188
ILE
186
A
SER
187
n
189
SER
187
A
LEU
188
n
190
LEU
188
A
PRO
189
n
191
PRO
189
A
TYR
190
n
192
TYR
190
A
ILE
191
n
193
ILE
191
A
GLU
192
n
194
GLU
192
A
LEU
193
n
195
LEU
193
A
PHE
194
n
196
PHE
194
A
ASN
195
n
197
ASN
195
A
THR
196
n
198
THR
196
A
ARG
197
n
199
ARG
197
A
SER
198
n
200
SER
198
A
ASN
199
n
201
ASN
199
A
ASN
200
n
202
ASN
200
A
PRO
201
n
203
PRO
201
A
ILE
202
n
204
ILE
202
A
VAL
203
n
205
VAL
203
A
ILE
204
n
206
ILE
204
A
PHE
205
n
207
PHE
205
A
GLN
206
n
208
GLN
206
A
GLN
207
n
209
GLN
207
A
SER
208
n
210
SER
208
A
LEU
209
n
211
LEU
209
A
LYS
210
n
212
LYS
210
A
VAL
211
n
213
VAL
211
A
LEU
212
n
214
LEU
212
A
MSE
213
n
215
MSE
213
A
SER
214
n
216
SER
214
A
PHE
215
n
217
PHE
215
A
ALA
216
n
218
ALA
216
A
LEU
217
n
219
LEU
217
A
LYS
218
n
220
LYS
218
A
2.1913
0.0637
0.2132
0.2299
-0.1989
1.3927
0.0578
0.0404
-0.1815
-0.0768
0.0010
0.0380
0.1709
-0.0127
-0.0588
-0.0095
0.0035
-0.0148
-0.0372
0.0026
-0.0020
refined
26.6160
9.5830
15.1480
X-RAY DIFFRACTION
3.1778
0.3137
1.2460
0.5989
0.2891
2.4612
0.1613
0.2623
-0.3739
-0.1068
-0.0484
0.0294
0.2864
0.1082
-0.1129
-0.0031
0.0362
-0.0244
-0.0446
-0.0391
-0.0257
refined
32.5960
5.4910
7.4730
X-RAY DIFFRACTION
4.9923
-2.5904
-0.7114
4.3767
0.7719
0.2843
0.1872
0.2620
0.0753
-0.2477
-0.2695
-0.2831
0.0542
0.2197
0.0822
-0.0335
0.0477
-0.0037
0.0200
0.0304
-0.0246
refined
49.0620
12.4710
15.2500
X-RAY DIFFRACTION
14.0341
0.4352
7.4310
3.1263
-0.0497
5.0128
0.0319
0.4957
0.1761
-0.0524
-0.0682
-0.1106
0.0412
0.1172
0.0363
-0.0273
-0.0029
0.0177
0.0124
0.0439
-0.0378
refined
35.6970
21.5490
7.2280
X-RAY DIFFRACTION
1.7296
-0.2496
0.8431
0.8111
-0.2328
0.9701
-0.0176
0.1019
0.1084
-0.0185
-0.0040
-0.0213
-0.0471
0.0480
0.0217
-0.0329
0.0060
0.0058
-0.0334
0.0170
-0.0141
refined
32.6780
19.5630
15.5570
X-RAY DIFFRACTION
0.9718
0.1537
0.2767
0.0383
-0.0997
1.5518
0.0044
-0.0180
0.0013
0.0505
-0.0060
-0.0468
-0.0793
-0.0404
0.0016
-0.0209
0.0115
0.0017
-0.0284
0.0007
0.0044
refined
25.6270
14.4810
30.7540
X-RAY DIFFRACTION
0.4622
0.3319
-0.0215
2.4960
0.1369
1.6210
0.0487
-0.0182
0.0629
0.0850
-0.0671
-0.0736
-0.0811
-0.0908
0.0185
-0.0527
0.0040
0.0028
-0.0276
-0.0071
-0.0029
refined
17.5090
14.8960
37.6540
X-RAY DIFFRACTION
1.0240
-0.1837
0.1237
4.9151
-3.0266
3.0065
0.0886
0.1171
0.0474
-0.0684
0.0599
0.1763
0.0283
-0.1245
-0.1485
-0.0573
0.0005
0.0051
-0.0029
0.0119
-0.0036
refined
15.1030
15.3550
21.2560
X-RAY DIFFRACTION
A
-1
A
1
A
45
A
47
X-RAY DIFFRACTION
1
A
46
A
48
A
78
A
80
X-RAY DIFFRACTION
2
A
79
A
81
A
94
A
96
X-RAY DIFFRACTION
3
A
95
A
97
A
105
A
107
X-RAY DIFFRACTION
4
A
106
A
108
A
141
A
143
X-RAY DIFFRACTION
5
A
142
A
144
A
181
A
183
X-RAY DIFFRACTION
6
A
182
A
184
A
203
A
205
X-RAY DIFFRACTION
7
A
204
A
206
A
218
A
220
X-RAY DIFFRACTION
8
author_and_software_defined_assembly
PISA
2
dimeric
3540
A
MSE
1
SELENOMETHIONINE
A
MSE
3
MET
A
MSE
131
SELENOMETHIONINE
A
MSE
133
MET
A
MSE
142
SELENOMETHIONINE
A
MSE
144
MET
A
MSE
213
SELENOMETHIONINE
A
MSE
215
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
2_656
-x+1,y,-z+1
crystal symmetry operation
68.2356349326
0.0000000000
68.2428787195
A
N
LEU
34
A
N
LEU
36
A
O
GLU
116
A
O
GLU
118
A
O
VAL
115
A
O
VAL
117
A
N
LEU
2
A
N
LEU
4
A
N
PHE
3
A
N
PHE
5
A
O
LYS
141
A
O
LYS
143
A
N
LEU
144
A
N
LEU
146
A
O
LYS
171
A
O
LYS
173
A
N
ILE
174
A
N
ILE
176
A
O
VAL
203
A
O
VAL
205
A
N
GLU
38
A
N
GLU
40
A
O
TYR
73
A
O
TYR
75
1
A
HOH
313
D
HOH
1
A
ASP
62
-161.69
105.11
1
A
SER
79
A
-65.19
-173.72
16.37
-0.71000
0.00000
-0.58000
-0.16000
0.00000
0.64000
0.975
0.967
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COOT program has also been used in refinement.
0.179
0.148
0.150
0.150
1.47
50.00
1769
35272
35272
5.000
99.030
2.190
0.043
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
0.000
0
SAD
0.065
0.068
0.80
0.80
1.20
MAXIMUM LIKELIHOOD
MASK
1.47
50.00
326
2057
2
0
1729
0.018
0.022
1849
0.005
0.020
1701
1.715
1.974
2528
0.876
3.000
3980
5.866
5.000
241
35.920
25.443
79
11.294
15.000
332
23.228
15.000
6
0.118
0.200
303
0.008
0.020
2091
0.003
0.020
347
0.231
0.200
383
0.200
0.200
1693
0.184
0.200
937
0.088
0.200
960
0.163
0.200
201
0.105
0.200
6
0.241
0.200
56
0.162
0.200
31
1.537
1.500
1400
0.356
1.500
466
1.655
2.000
1902
2.896
3.000
742
4.139
4.500
626
0.288
0.211
1.51
119
2298
20
91.35
19.80
1.470
50.000
2QMO
35286
35286
-3.000
0.069
0.069
1
48.7540
7.700
99.0
0.444
1.47
1.52
3.10
0.444
1
5.20
91.3
phasing
HKL-3000
phasing
MLPHARE
model building
DM
phasing
SHELXD
model building
ARP/wARP
refinement
REFMAC
5.2.0005
data collection
HKL-3000
data reduction
HKL-2000
data scaling
HKL-2000
phasing
DM
model building
SHELXE
phasing
RESOLVE
model building
O
model building
Coot
phasing
CCP4
Crystal structure of dethiobiotin synthetase (bioD) from Helicobacter pylori
1
N
N
2
N
N
2
N
N
3
N
N
A
GLY
12
A
GLY
14
HELX_P
A
CYS
27
A
CYS
29
1
1
16
A
SER
49
A
SER
51
HELX_P
A
ARG
59
A
ARG
61
1
2
11
A
THR
66
A
THR
68
HELX_P
A
SER
71
A
SER
73
1
3
6
A
ALA
80
A
ALA
82
HELX_P
A
ASP
89
A
ASP
91
1
4
10
A
ASP
95
A
ASP
97
HELX_P
A
PHE
106
A
PHE
108
1
5
12
A
THR
107
A
THR
109
HELX_P
A
THR
109
A
THR
111
5
6
3
A
ASN
130
A
ASN
132
HELX_P
A
LYS
139
A
LYS
141
1
7
10
A
GLY
151
A
GLY
153
HELX_P
A
SER
165
A
SER
167
1
8
15
A
ALA
182
A
ALA
184
HELX_P
A
SER
187
A
SER
189
1
9
6
A
SER
187
A
SER
189
HELX_P
A
SER
198
A
SER
200
1
10
12
A
SER
208
A
SER
210
HELX_P
A
LYS
218
A
LYS
220
1
11
11
covale
1.315
both
A
HIS
0
A
C
HIS
2
1_555
A
MSE
1
A
N
MSE
3
1_555
covale
1.329
both
A
MSE
1
A
C
MSE
3
1_555
A
LEU
2
A
N
LEU
4
1_555
covale
1.338
both
A
ASN
130
A
C
ASN
132
1_555
A
MSE
131
A
N
MSE
133
1_555
covale
1.322
both
A
MSE
131
A
C
MSE
133
1_555
A
LEU
132
A
N
LEU
134
1_555
covale
1.325
both
A
LYS
141
A
C
LYS
143
1_555
A
MSE
142
A
N
MSE
144
1_555
covale
1.342
both
A
MSE
142
A
C
MSE
144
1_555
A
LEU
143
A
N
LEU
145
1_555
covale
1.338
both
A
LEU
212
A
C
LEU
214
1_555
A
MSE
213
A
N
MSE
215
1_555
covale
1.353
both
A
MSE
213
A
C
MSE
215
1_555
A
SER
214
A
N
SER
216
1_555
LIGASE
dethiobiotin synthetase, structural genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, ATP-binding, Biotin biosynthesis, Ligase, Magnesium, Nucleotide-binding
A
GLY
-1
A
GLY
1
1
A
HIS
0
A
HIS
2
-3.27
BIOD_HELPY
UNP
1
1
O24872
MLFISATNTNAGKTTCARLLAQYCNACGVKTILLKPIETGVNDAINHSSDAHLFLQDNRLLDRSLTLKDISFYRYHKVSA
PLIAQQEEDPNAPIDTDNLTQRLHNFTKTYDLVIVEGAGGLCVPITLEENMLDFALKLKAKMLLISHDNLGLINDCLLND
FLLKSHQLDYKIAINLKGNNTAFHSISLPYIELFNTRSNNPIVIFQQSLKVLMSFALK
1
218
2QMO
1
218
O24872
A
1
3
220
1
expression tag
GLY
-1
2QMO
A
O24872
UNP
1
1
expression tag
HIS
0
2QMO
A
O24872
UNP
2
1
MET
modified residue
MSE
1
2QMO
A
O24872
UNP
1
3
1
MET
modified residue
MSE
131
2QMO
A
O24872
UNP
131
133
1
MET
modified residue
MSE
142
2QMO
A
O24872
UNP
142
144
1
MET
modified residue
MSE
213
2QMO
A
O24872
UNP
213
215
6
2
parallel
parallel
parallel
parallel
parallel
parallel
A
THR
31
A
THR
33
A
LEU
34
A
LEU
36
A
LEU
112
A
LEU
114
A
GLU
116
A
GLU
118
A
MSE
1
A
MSE
3
A
ALA
6
A
ALA
8
A
LYS
141
A
LYS
143
A
SER
146
A
SER
148
A
TYR
170
A
TYR
172
A
ILE
174
A
ILE
176
A
VAL
203
A
VAL
205
A
ILE
204
A
ILE
206
A
ILE
37
A
ILE
39
A
GLU
38
A
GLU
40
A
TYR
73
A
TYR
75
A
ARG
74
A
ARG
76
BINDING SITE FOR RESIDUE CL A 301
A
CL
301
Software
4
BINDING SITE FOR RESIDUE CL A 302
A
CL
302
Software
3
A
GLY
151
A
GLY
153
4
1_555
A
LEU
152
A
LEU
154
4
1_555
A
ILE
153
A
ILE
155
4
1_555
A
SER
187
A
SER
189
4
1_555
A
LYS
13
A
LYS
15
3
1_555
A
THR
14
A
THR
16
3
1_555
A
HOH
517
D
HOH
3
1_555
5
C 1 2 1