0.010042
0.000000
0.000000
-0.000000
0.024686
0.000000
0.000000
-0.000000
0.016444
0.000000
0.000000
0.000000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
90.000
90.000
99.577
40.509
60.813
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
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 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
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
To be published
0353
Crystal structure of a putative TonB-dependent receptor (PA5505) from Pseudomonas aeruginosa PAO1 at 1.60 A resolution
10.2210/pdb4k3f/pdb
pdb_00004k3f
100
1
Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
PIXEL
2013-04-01
DECTRIS PILATUS 6M
double crystal Si(111)
MAD
M
x-ray
1
0.8265
1.0
0.9794
1.0
0.9792
1.0
BL12-2
SSRL
0.8265,0.9794,0.9792
SYNCHROTRON
SSRL BEAMLINE BL12-2
26221.766
Probable TonB-dependent receptor
1
man
polymer
196.106
SELENOMETHIONINE
1
syn
non-polymer
35.453
CHLORIDE ION
1
syn
non-polymer
96.063
SULFATE ION
2
syn
non-polymer
92.094
GLYCEROL
5
syn
non-polymer
18.015
water
257
nat
water
no
yes
GAESLTVAATPVPHAEILNVVKPLLAKEGVDLKIKEFTDYVQPNVQVSEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGV
HIEPLGAYSSKYKKLDELPSGATVVIPNDATNGGRALLLLDKAGVIKLKDNKSITATPKDIVDNPKNIKIRELEAATLPR
VLTQVD(MSE)ALINTNYALEAKLNPTKDALAIEGSDSPYVNILVARPDNKDSDA(MSE)QKLAKALHSAEIKQFIQEKY
KGAVVPAF
GAESLTVAATPVPHAEILNVVKPLLAKEGVDLKIKEFTDYVQPNVQVSEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGV
HIEPLGAYSSKYKKLDELPSGATVVIPNDATNGGRALLLLDKAGVIKLKDNKSITATPKDIVDNPKNIKIRELEAATLPR
VLTQVDMALINTNYALEAKLNPTKDALAIEGSDSPYVNILVARPDNKDSDAMQKLAKALHSAEIKQFIQEKYKGAVVPAF
A
JCSG-417287
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
PAO1
sample
PA5505
208964
Pseudomonas aeruginosa
562
Escherichia Coli
PB1
Plasmid
SpeedET
1
2.34
47.41
VAPOR DIFFUSION, SITTING DROP
7.0
3.20M ammonium sulfate, 0.7% n-Butanol, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
Joint Center for Structural Genomics
JCSG
PSI:Biology
software
citation_author
database_2
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Refinement description
Database references
Database references
Derived calculations
1
0
2013-04-24
1
1
2017-11-15
1
2
2018-01-24
1
3
2023-02-01
_software.classification
_software.name
_citation_author.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
RCSB
Y
RCSB
2013-04-10
REL
REL
MSE
SELENOMETHIONINE
CL
CHLORIDE ION
SO4
SULFATE ION
GOL
GLYCEROL
HOH
water
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 22-260 OF THE TARGET SEQUENCE.
MSE
300
2
MSE
MSE
300
A
CL
301
3
CL
CL
301
A
SO4
302
4
SO4
SO4
302
A
SO4
303
4
SO4
SO4
303
A
GOL
304
5
GOL
GOL
304
A
GOL
305
5
GOL
GOL
305
A
GOL
306
5
GOL
GOL
306
A
GOL
307
5
GOL
GOL
307
A
GOL
308
5
GOL
GOL
308
A
HOH
309
6
HOH
HOH
401
A
HOH
310
6
HOH
HOH
402
A
HOH
311
6
HOH
HOH
403
A
HOH
312
6
HOH
HOH
404
A
HOH
313
6
HOH
HOH
405
A
HOH
314
6
HOH
HOH
406
A
HOH
315
6
HOH
HOH
407
A
HOH
316
6
HOH
HOH
408
A
HOH
317
6
HOH
HOH
409
A
HOH
318
6
HOH
HOH
410
A
HOH
319
6
HOH
HOH
411
A
HOH
320
6
HOH
HOH
412
A
HOH
321
6
HOH
HOH
413
A
HOH
322
6
HOH
HOH
414
A
HOH
323
6
HOH
HOH
415
A
HOH
324
6
HOH
HOH
416
A
HOH
325
6
HOH
HOH
417
A
HOH
326
6
HOH
HOH
418
A
HOH
327
6
HOH
HOH
419
A
HOH
328
6
HOH
HOH
420
A
HOH
329
6
HOH
HOH
421
A
HOH
330
6
HOH
HOH
422
A
HOH
331
6
HOH
HOH
423
A
HOH
332
6
HOH
HOH
424
A
HOH
333
6
HOH
HOH
425
A
HOH
334
6
HOH
HOH
426
A
HOH
335
6
HOH
HOH
427
A
HOH
336
6
HOH
HOH
428
A
HOH
337
6
HOH
HOH
429
A
HOH
338
6
HOH
HOH
430
A
HOH
339
6
HOH
HOH
431
A
HOH
340
6
HOH
HOH
432
A
HOH
341
6
HOH
HOH
433
A
HOH
342
6
HOH
HOH
434
A
HOH
343
6
HOH
HOH
435
A
HOH
344
6
HOH
HOH
436
A
HOH
345
6
HOH
HOH
437
A
HOH
346
6
HOH
HOH
438
A
HOH
347
6
HOH
HOH
439
A
HOH
348
6
HOH
HOH
440
A
HOH
349
6
HOH
HOH
441
A
HOH
350
6
HOH
HOH
442
A
HOH
351
6
HOH
HOH
443
A
HOH
352
6
HOH
HOH
444
A
HOH
353
6
HOH
HOH
445
A
HOH
354
6
HOH
HOH
446
A
HOH
355
6
HOH
HOH
447
A
HOH
356
6
HOH
HOH
448
A
HOH
357
6
HOH
HOH
449
A
HOH
358
6
HOH
HOH
450
A
HOH
359
6
HOH
HOH
451
A
HOH
360
6
HOH
HOH
452
A
HOH
361
6
HOH
HOH
453
A
HOH
362
6
HOH
HOH
454
A
HOH
363
6
HOH
HOH
455
A
HOH
364
6
HOH
HOH
456
A
HOH
365
6
HOH
HOH
457
A
HOH
366
6
HOH
HOH
458
A
HOH
367
6
HOH
HOH
459
A
HOH
368
6
HOH
HOH
460
A
HOH
369
6
HOH
HOH
461
A
HOH
370
6
HOH
HOH
462
A
HOH
371
6
HOH
HOH
463
A
HOH
372
6
HOH
HOH
464
A
HOH
373
6
HOH
HOH
465
A
HOH
374
6
HOH
HOH
466
A
HOH
375
6
HOH
HOH
467
A
HOH
376
6
HOH
HOH
468
A
HOH
377
6
HOH
HOH
469
A
HOH
378
6
HOH
HOH
470
A
HOH
379
6
HOH
HOH
471
A
HOH
380
6
HOH
HOH
472
A
HOH
381
6
HOH
HOH
473
A
HOH
382
6
HOH
HOH
474
A
HOH
383
6
HOH
HOH
475
A
HOH
384
6
HOH
HOH
476
A
HOH
385
6
HOH
HOH
477
A
HOH
386
6
HOH
HOH
478
A
HOH
387
6
HOH
HOH
479
A
HOH
388
6
HOH
HOH
480
A
HOH
389
6
HOH
HOH
481
A
HOH
390
6
HOH
HOH
482
A
HOH
391
6
HOH
HOH
483
A
HOH
392
6
HOH
HOH
484
A
HOH
393
6
HOH
HOH
485
A
HOH
394
6
HOH
HOH
486
A
HOH
395
6
HOH
HOH
487
A
HOH
396
6
HOH
HOH
488
A
HOH
397
6
HOH
HOH
489
A
HOH
398
6
HOH
HOH
490
A
HOH
399
6
HOH
HOH
491
A
HOH
400
6
HOH
HOH
492
A
HOH
401
6
HOH
HOH
493
A
HOH
402
6
HOH
HOH
494
A
HOH
403
6
HOH
HOH
495
A
HOH
404
6
HOH
HOH
496
A
HOH
405
6
HOH
HOH
497
A
HOH
406
6
HOH
HOH
498
A
HOH
407
6
HOH
HOH
499
A
HOH
408
6
HOH
HOH
500
A
HOH
409
6
HOH
HOH
501
A
HOH
410
6
HOH
HOH
502
A
HOH
411
6
HOH
HOH
503
A
HOH
412
6
HOH
HOH
504
A
HOH
413
6
HOH
HOH
505
A
HOH
414
6
HOH
HOH
506
A
HOH
415
6
HOH
HOH
507
A
HOH
416
6
HOH
HOH
508
A
HOH
417
6
HOH
HOH
509
A
HOH
418
6
HOH
HOH
510
A
HOH
419
6
HOH
HOH
511
A
HOH
420
6
HOH
HOH
512
A
HOH
421
6
HOH
HOH
513
A
HOH
422
6
HOH
HOH
514
A
HOH
423
6
HOH
HOH
515
A
HOH
424
6
HOH
HOH
516
A
HOH
425
6
HOH
HOH
517
A
HOH
426
6
HOH
HOH
518
A
HOH
427
6
HOH
HOH
519
A
HOH
428
6
HOH
HOH
520
A
HOH
429
6
HOH
HOH
521
A
HOH
430
6
HOH
HOH
522
A
HOH
431
6
HOH
HOH
523
A
HOH
432
6
HOH
HOH
524
A
HOH
433
6
HOH
HOH
525
A
HOH
434
6
HOH
HOH
526
A
HOH
435
6
HOH
HOH
527
A
HOH
436
6
HOH
HOH
528
A
HOH
437
6
HOH
HOH
529
A
HOH
438
6
HOH
HOH
530
A
HOH
439
6
HOH
HOH
531
A
HOH
440
6
HOH
HOH
532
A
HOH
441
6
HOH
HOH
533
A
HOH
442
6
HOH
HOH
534
A
HOH
443
6
HOH
HOH
535
A
HOH
444
6
HOH
HOH
536
A
HOH
445
6
HOH
HOH
537
A
HOH
446
6
HOH
HOH
538
A
HOH
447
6
HOH
HOH
539
A
HOH
448
6
HOH
HOH
540
A
HOH
449
6
HOH
HOH
541
A
HOH
450
6
HOH
HOH
542
A
HOH
451
6
HOH
HOH
543
A
HOH
452
6
HOH
HOH
544
A
HOH
453
6
HOH
HOH
545
A
HOH
454
6
HOH
HOH
546
A
HOH
455
6
HOH
HOH
547
A
HOH
456
6
HOH
HOH
548
A
HOH
457
6
HOH
HOH
549
A
HOH
458
6
HOH
HOH
550
A
HOH
459
6
HOH
HOH
551
A
HOH
460
6
HOH
HOH
552
A
HOH
461
6
HOH
HOH
553
A
HOH
462
6
HOH
HOH
554
A
HOH
463
6
HOH
HOH
555
A
HOH
464
6
HOH
HOH
556
A
HOH
465
6
HOH
HOH
557
A
HOH
466
6
HOH
HOH
558
A
HOH
467
6
HOH
HOH
559
A
HOH
468
6
HOH
HOH
560
A
HOH
469
6
HOH
HOH
561
A
HOH
470
6
HOH
HOH
562
A
HOH
471
6
HOH
HOH
563
A
HOH
472
6
HOH
HOH
564
A
HOH
473
6
HOH
HOH
565
A
HOH
474
6
HOH
HOH
566
A
HOH
475
6
HOH
HOH
567
A
HOH
476
6
HOH
HOH
568
A
HOH
477
6
HOH
HOH
569
A
HOH
478
6
HOH
HOH
570
A
HOH
479
6
HOH
HOH
571
A
HOH
480
6
HOH
HOH
572
A
HOH
481
6
HOH
HOH
573
A
HOH
482
6
HOH
HOH
574
A
HOH
483
6
HOH
HOH
575
A
HOH
484
6
HOH
HOH
576
A
HOH
485
6
HOH
HOH
577
A
HOH
486
6
HOH
HOH
578
A
HOH
487
6
HOH
HOH
579
A
HOH
488
6
HOH
HOH
580
A
HOH
489
6
HOH
HOH
581
A
HOH
490
6
HOH
HOH
582
A
HOH
491
6
HOH
HOH
583
A
HOH
492
6
HOH
HOH
584
A
HOH
493
6
HOH
HOH
585
A
HOH
494
6
HOH
HOH
586
A
HOH
495
6
HOH
HOH
587
A
HOH
496
6
HOH
HOH
588
A
HOH
497
6
HOH
HOH
589
A
HOH
498
6
HOH
HOH
590
A
HOH
499
6
HOH
HOH
591
A
HOH
500
6
HOH
HOH
592
A
HOH
501
6
HOH
HOH
593
A
HOH
502
6
HOH
HOH
594
A
HOH
503
6
HOH
HOH
595
A
HOH
504
6
HOH
HOH
596
A
HOH
505
6
HOH
HOH
597
A
HOH
506
6
HOH
HOH
598
A
HOH
507
6
HOH
HOH
599
A
HOH
508
6
HOH
HOH
600
A
HOH
509
6
HOH
HOH
601
A
HOH
510
6
HOH
HOH
602
A
HOH
511
6
HOH
HOH
603
A
HOH
512
6
HOH
HOH
604
A
HOH
513
6
HOH
HOH
605
A
HOH
514
6
HOH
HOH
606
A
HOH
515
6
HOH
HOH
607
A
HOH
516
6
HOH
HOH
608
A
HOH
517
6
HOH
HOH
609
A
HOH
518
6
HOH
HOH
610
A
HOH
519
6
HOH
HOH
611
A
HOH
520
6
HOH
HOH
612
A
HOH
521
6
HOH
HOH
613
A
HOH
522
6
HOH
HOH
614
A
HOH
523
6
HOH
HOH
615
A
HOH
524
6
HOH
HOH
616
A
HOH
525
6
HOH
HOH
617
A
HOH
526
6
HOH
HOH
618
A
HOH
527
6
HOH
HOH
619
A
HOH
528
6
HOH
HOH
620
A
HOH
529
6
HOH
HOH
621
A
HOH
530
6
HOH
HOH
622
A
HOH
531
6
HOH
HOH
623
A
HOH
532
6
HOH
HOH
624
A
HOH
533
6
HOH
HOH
625
A
HOH
534
6
HOH
HOH
626
A
HOH
535
6
HOH
HOH
627
A
HOH
536
6
HOH
HOH
628
A
HOH
537
6
HOH
HOH
629
A
HOH
538
6
HOH
HOH
630
A
HOH
539
6
HOH
HOH
631
A
HOH
540
6
HOH
HOH
632
A
HOH
541
6
HOH
HOH
633
A
HOH
542
6
HOH
HOH
634
A
HOH
543
6
HOH
HOH
635
A
HOH
544
6
HOH
HOH
636
A
HOH
545
6
HOH
HOH
637
A
HOH
546
6
HOH
HOH
638
A
HOH
547
6
HOH
HOH
639
A
HOH
548
6
HOH
HOH
640
A
HOH
549
6
HOH
HOH
641
A
HOH
550
6
HOH
HOH
642
A
HOH
551
6
HOH
HOH
643
A
HOH
552
6
HOH
HOH
644
A
HOH
553
6
HOH
HOH
645
A
HOH
554
6
HOH
HOH
646
A
HOH
555
6
HOH
HOH
647
A
HOH
556
6
HOH
HOH
648
A
HOH
557
6
HOH
HOH
649
A
HOH
558
6
HOH
HOH
650
A
HOH
559
6
HOH
HOH
651
A
HOH
560
6
HOH
HOH
652
A
HOH
561
6
HOH
HOH
653
A
HOH
562
6
HOH
HOH
654
A
HOH
563
6
HOH
HOH
655
A
HOH
564
6
HOH
HOH
656
A
HOH
565
6
HOH
HOH
657
A
GLY
0
n
1
GLY
0
A
ALA
22
n
2
ALA
22
A
GLU
23
n
3
GLU
23
A
SER
24
n
4
SER
24
A
LEU
25
n
5
LEU
25
A
THR
26
n
6
THR
26
A
VAL
27
n
7
VAL
27
A
ALA
28
n
8
ALA
28
A
ALA
29
n
9
ALA
29
A
THR
30
n
10
THR
30
A
PRO
31
n
11
PRO
31
A
VAL
32
n
12
VAL
32
A
PRO
33
n
13
PRO
33
A
HIS
34
n
14
HIS
34
A
ALA
35
n
15
ALA
35
A
GLU
36
n
16
GLU
36
A
ILE
37
n
17
ILE
37
A
LEU
38
n
18
LEU
38
A
ASN
39
n
19
ASN
39
A
VAL
40
n
20
VAL
40
A
VAL
41
n
21
VAL
41
A
LYS
42
n
22
LYS
42
A
PRO
43
n
23
PRO
43
A
LEU
44
n
24
LEU
44
A
LEU
45
n
25
LEU
45
A
ALA
46
n
26
ALA
46
A
LYS
47
n
27
LYS
47
A
GLU
48
n
28
GLU
48
A
GLY
49
n
29
GLY
49
A
VAL
50
n
30
VAL
50
A
ASP
51
n
31
ASP
51
A
LEU
52
n
32
LEU
52
A
LYS
53
n
33
LYS
53
A
ILE
54
n
34
ILE
54
A
LYS
55
n
35
LYS
55
A
GLU
56
n
36
GLU
56
A
PHE
57
n
37
PHE
57
A
THR
58
n
38
THR
58
A
ASP
59
n
39
ASP
59
A
TYR
60
n
40
TYR
60
A
VAL
61
n
41
VAL
61
A
GLN
62
n
42
GLN
62
A
PRO
63
n
43
PRO
63
A
ASN
64
n
44
ASN
64
A
VAL
65
n
45
VAL
65
A
GLN
66
n
46
GLN
66
A
VAL
67
n
47
VAL
67
A
SER
68
n
48
SER
68
A
GLU
69
n
49
GLU
69
A
LYS
70
n
50
LYS
70
A
ARG
71
n
51
ARG
71
A
LEU
72
n
52
LEU
72
A
ASP
73
n
53
ASP
73
A
ALA
74
n
54
ALA
74
A
ASN
75
n
55
ASN
75
A
PHE
76
n
56
PHE
76
A
PHE
77
n
57
PHE
77
A
GLN
78
n
58
GLN
78
A
HIS
79
n
59
HIS
79
A
GLN
80
n
60
GLN
80
A
PRO
81
n
61
PRO
81
A
TYR
82
n
62
TYR
82
A
LEU
83
n
63
LEU
83
A
ASP
84
n
64
ASP
84
A
GLU
85
n
65
GLU
85
A
PHE
86
n
66
PHE
86
A
ASN
87
n
67
ASN
87
A
LYS
88
n
68
LYS
88
A
ALA
89
n
69
ALA
89
A
LYS
90
n
70
LYS
90
A
GLY
91
n
71
GLY
91
A
THR
92
n
72
THR
92
A
ASP
93
n
73
ASP
93
A
LEU
94
n
74
LEU
94
A
VAL
95
n
75
VAL
95
A
ALA
96
n
76
ALA
96
A
VAL
97
n
77
VAL
97
A
THR
98
n
78
THR
98
A
GLY
99
n
79
GLY
99
A
VAL
100
n
80
VAL
100
A
HIS
101
n
81
HIS
101
A
ILE
102
n
82
ILE
102
A
GLU
103
n
83
GLU
103
A
PRO
104
n
84
PRO
104
A
LEU
105
n
85
LEU
105
A
GLY
106
n
86
GLY
106
A
ALA
107
n
87
ALA
107
A
TYR
108
n
88
TYR
108
A
SER
109
n
89
SER
109
A
SER
110
n
90
SER
110
A
LYS
111
n
91
LYS
111
A
TYR
112
n
92
TYR
112
A
LYS
113
n
93
LYS
113
A
LYS
114
n
94
LYS
114
A
LEU
115
n
95
LEU
115
A
ASP
116
n
96
ASP
116
A
GLU
117
n
97
GLU
117
A
LEU
118
n
98
LEU
118
A
PRO
119
n
99
PRO
119
A
SER
120
n
100
SER
120
A
GLY
121
n
101
GLY
121
A
ALA
122
n
102
ALA
122
A
THR
123
n
103
THR
123
A
VAL
124
n
104
VAL
124
A
VAL
125
n
105
VAL
125
A
ILE
126
n
106
ILE
126
A
PRO
127
n
107
PRO
127
A
ASN
128
n
108
ASN
128
A
ASP
129
n
109
ASP
129
A
ALA
130
n
110
ALA
130
A
THR
131
n
111
THR
131
A
ASN
132
n
112
ASN
132
A
GLY
133
n
113
GLY
133
A
GLY
134
n
114
GLY
134
A
ARG
135
n
115
ARG
135
A
ALA
136
n
116
ALA
136
A
LEU
137
n
117
LEU
137
A
LEU
138
n
118
LEU
138
A
LEU
139
n
119
LEU
139
A
LEU
140
n
120
LEU
140
A
ASP
141
n
121
ASP
141
A
LYS
142
n
122
LYS
142
A
ALA
143
n
123
ALA
143
A
GLY
144
n
124
GLY
144
A
VAL
145
n
125
VAL
145
A
ILE
146
n
126
ILE
146
A
LYS
147
n
127
LYS
147
A
LEU
148
n
128
LEU
148
A
LYS
149
n
129
LYS
149
A
ASP
150
n
130
ASP
150
A
ASN
151
n
131
ASN
151
A
LYS
152
n
132
LYS
152
A
SER
153
n
133
SER
153
A
ILE
154
n
134
ILE
154
A
THR
155
n
135
THR
155
A
ALA
156
n
136
ALA
156
A
THR
157
n
137
THR
157
A
PRO
158
n
138
PRO
158
A
LYS
159
n
139
LYS
159
A
ASP
160
n
140
ASP
160
A
ILE
161
n
141
ILE
161
A
VAL
162
n
142
VAL
162
A
ASP
163
n
143
ASP
163
A
ASN
164
n
144
ASN
164
A
PRO
165
n
145
PRO
165
A
LYS
166
n
146
LYS
166
A
ASN
167
n
147
ASN
167
A
ILE
168
n
148
ILE
168
A
LYS
169
n
149
LYS
169
A
ILE
170
n
150
ILE
170
A
ARG
171
n
151
ARG
171
A
GLU
172
n
152
GLU
172
A
LEU
173
n
153
LEU
173
A
GLU
174
n
154
GLU
174
A
ALA
175
n
155
ALA
175
A
ALA
176
n
156
ALA
176
A
THR
177
n
157
THR
177
A
LEU
178
n
158
LEU
178
A
PRO
179
n
159
PRO
179
A
ARG
180
n
160
ARG
180
A
VAL
181
n
161
VAL
181
A
LEU
182
n
162
LEU
182
A
THR
183
n
163
THR
183
A
GLN
184
n
164
GLN
184
A
VAL
185
n
165
VAL
185
A
ASP
186
n
166
ASP
186
A
MSE
187
n
167
MSE
187
A
ALA
188
n
168
ALA
188
A
LEU
189
n
169
LEU
189
A
ILE
190
n
170
ILE
190
A
ASN
191
n
171
ASN
191
A
THR
192
n
172
THR
192
A
ASN
193
n
173
ASN
193
A
TYR
194
n
174
TYR
194
A
ALA
195
n
175
ALA
195
A
LEU
196
n
176
LEU
196
A
GLU
197
n
177
GLU
197
A
ALA
198
n
178
ALA
198
A
LYS
199
n
179
LYS
199
A
LEU
200
n
180
LEU
200
A
ASN
201
n
181
ASN
201
A
PRO
202
n
182
PRO
202
A
THR
203
n
183
THR
203
A
LYS
204
n
184
LYS
204
A
ASP
205
n
185
ASP
205
A
ALA
206
n
186
ALA
206
A
LEU
207
n
187
LEU
207
A
ALA
208
n
188
ALA
208
A
ILE
209
n
189
ILE
209
A
GLU
210
n
190
GLU
210
A
GLY
211
n
191
GLY
211
A
SER
212
n
192
SER
212
A
ASP
213
n
193
ASP
213
A
SER
214
n
194
SER
214
A
PRO
215
n
195
PRO
215
A
TYR
216
n
196
TYR
216
A
VAL
217
n
197
VAL
217
A
ASN
218
n
198
ASN
218
A
ILE
219
n
199
ILE
219
A
LEU
220
n
200
LEU
220
A
VAL
221
n
201
VAL
221
A
ALA
222
n
202
ALA
222
A
ARG
223
n
203
ARG
223
A
PRO
224
n
204
PRO
224
A
ASP
225
n
205
ASP
225
A
ASN
226
n
206
ASN
226
A
LYS
227
n
207
LYS
227
A
ASP
228
n
208
ASP
228
A
SER
229
n
209
SER
229
A
ASP
230
n
210
ASP
230
A
ALA
231
n
211
ALA
231
A
MSE
232
n
212
MSE
232
A
GLN
233
n
213
GLN
233
A
LYS
234
n
214
LYS
234
A
LEU
235
n
215
LEU
235
A
ALA
236
n
216
ALA
236
A
LYS
237
n
217
LYS
237
A
ALA
238
n
218
ALA
238
A
LEU
239
n
219
LEU
239
A
HIS
240
n
220
HIS
240
A
SER
241
n
221
SER
241
A
ALA
242
n
222
ALA
242
A
GLU
243
n
223
GLU
243
A
ILE
244
n
224
ILE
244
A
LYS
245
n
225
LYS
245
A
GLN
246
n
226
GLN
246
A
PHE
247
n
227
PHE
247
A
ILE
248
n
228
ILE
248
A
GLN
249
n
229
GLN
249
A
GLU
250
n
230
GLU
250
A
LYS
251
n
231
LYS
251
A
TYR
252
n
232
TYR
252
A
LYS
253
n
233
LYS
253
A
GLY
254
n
234
GLY
254
A
ALA
255
n
235
ALA
255
A
VAL
256
n
236
VAL
256
A
VAL
257
n
237
VAL
257
A
PRO
258
n
238
PRO
258
A
ALA
259
n
239
ALA
259
A
PHE
260
n
240
PHE
260
A
0.1378
0.0644
0.0397
0.4739
0.2792
0.7150
-0.0001
-0.0080
-0.0068
0.0321
-0.0199
0.0453
-0.0216
-0.0580
0.0200
0.0138
0.0084
0.0088
0.0096
0.0021
0.0107
refined
15.3590
8.7600
12.8430
X-RAY DIFFRACTION
A
0
A
260
X-RAY DIFFRACTION
1
author_and_software_defined_assembly
PISA
1
monomeric
A
MSE
187
SELENOMETHIONINE
A
MSE
167
MET
A
MSE
232
SELENOMETHIONINE
A
MSE
212
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
A
O
ASP
51
A
O
ASP
31
A
N
GLU
23
A
N
GLU
3
A
N
ALA
28
A
N
ALA
8
A
O
PHE
76
A
O
PHE
56
A
N
ASN
75
A
N
ASN
55
A
O
VAL
221
A
O
VAL
201
A
O
ASN
218
A
O
ASN
198
A
N
HIS
101
A
N
HIS
81
A
N
ILE
102
A
N
ILE
82
A
O
VAL
257
A
O
VAL
237
A
O
ARG
171
A
O
ARG
151
A
N
VAL
124
A
N
VAL
104
A
N
VAL
125
A
N
VAL
105
A
O
MSE
187
A
O
MSE
167
A
O
ALA
188
A
O
ALA
168
A
N
TYR
108
A
N
TYR
88
A
N
ALA
107
A
N
ALA
87
A
O
ALA
208
A
O
ALA
188
A
N
LYS
147
A
N
LYS
127
A
O
VAL
162
A
O
VAL
142
1
A
HOH
499
K
HOH
1
A
CG
LYS
113
A
CG
LYS
93
1
Y
1
A
CD
LYS
113
A
CD
LYS
93
1
Y
1
A
CE
LYS
113
A
CE
LYS
93
1
Y
1
A
NZ
LYS
113
A
NZ
LYS
93
1
Y
1
A
CG
LYS
159
A
CG
LYS
139
1
Y
1
A
CD
LYS
159
A
CD
LYS
139
1
Y
1
A
CE
LYS
159
A
CE
LYS
139
1
Y
1
A
NZ
LYS
159
A
NZ
LYS
139
1
Y
1
A
A
O
O
HOH
HOH
568
636
2.17
1
A
PHE
77
-167.34
-16.68
1
A
VAL
100
-120.74
-55.15
1
A
ALA
222
-147.09
-151.19
93.630
22.2558
9.350
0.9500
-0.0000
-0.0000
-0.6800
-0.0000
-0.2800
0.9740
0.9650
1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 6. SULFATE ION (SO4) AND GLYCEROL (GOL) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. 7. A SELENOMETHIONINE AMINO ACID IS BOUND TO THE PROTEIN. ANOMALOUS DIFFERENCE FOURIER MAP CONFIRMS THIS METHIONINE TO BE SELENOMETHIONINE.
0.1847
0.1506
0.1523
1.6000
29.135
1641
32319
5.1000
97.0700
1.000
0.300
2.9450
0.0550
RANDOM
1
THROUGHOUT
0.000
MAD
0.0790
0.0820
0.8000
0.8000
1.2000
MAXIMUM LIKELIHOOD WITH PHASES
BABINET MODEL WITH MASK
1.6000
29.135
257
2139
50
0
1832
0.012
0.019
2004
0.001
0.020
2013
1.536
2.013
2729
0.812
3.000
4669
5.903
5.000
261
42.163
26.329
79
13.063
15.000
354
15.994
15.000
6
0.097
0.200
326
0.008
0.021
2248
0.001
0.020
386
1.826
3.077
1007
1.827
3.078
1006
2.415
5.766
1269
0.3590
0.2770
1.6410
129
2242
2371
20
98.3800
19.747
1.60
29.135
4K3F
32359
-3.000
0.056
1
9.160
92.400
0.467
1.600
1.660
1.9
11216
6048
1
92.100
0.396
1.660
1.720
2.3
9814
5320
1
93.300
0.298
1.720
1.800
3.0
10914
6029
1
93.400
0.231
1.800
1.900
3.9
10830
6052
1
91.600
0.159
1.900
2.020
5.6
11279
5967
1
94.500
0.105
2.020
2.170
8.2
10712
5667
1
93.800
0.074
2.170
2.390
10.3
10417
5811
1
91.600
0.059
2.390
2.730
13.0
11324
5838
1
94.000
0.040
2.730
3.440
17.8
10814
5764
1
91.000
0.025
3.440
26.4
11142
5655
1
88.900
model building
D.C. & J.S. Richardson lab
molprobity@kinemage.biochem.duke.edu
http://kinemage.biochem.duke.edu/molprobity/
MolProbity
package
3beta29
data extraction
PDB
deposit@deposit.rcsb.org
June 10, 2010
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.10
phasing
George M. Sheldrick
gsheldr@shelx.uni-ac.gwdg.de
Fortran_77
http://shelx.uni-ac.gwdg.de/SHELX/
SHELX
package
phasing
Eric de La Fortelle
sharp-develop@globalphasing.com
http://www.globalphasing.com/sharp/
SHARP
package
data scaling
Wolfgang Kabsch
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html
XSCALE
package
July 4, 2012
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
5.7.0032
data reduction
XDS
phasing
SHELXD
Crystal structure of a putative TonB-dependent receptor (PA5505) from Pseudomonas aeruginosa PAO1 at 1.60 A resolution
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
5
N
N
5
N
N
5
N
N
5
N
N
5
N
N
6
N
N
CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
A
PRO
33
A
PRO
13
HELX_P
A
LYS
47
A
LYS
27
1
1
15
A
VAL
61
A
VAL
41
HELX_P
A
GLU
69
A
GLU
49
1
2
9
A
GLN
80
A
GLN
60
HELX_P
A
GLY
91
A
GLY
71
1
3
12
A
LYS
114
A
LYS
94
HELX_P
A
LEU
118
A
LEU
98
5
4
5
A
ASP
129
A
ASP
109
HELX_P
A
ALA
143
A
ALA
123
1
5
15
A
THR
157
A
THR
137
HELX_P
A
LYS
159
A
LYS
139
5
6
3
A
GLU
174
A
GLU
154
HELX_P
A
ALA
176
A
ALA
156
5
7
3
A
THR
177
A
THR
157
HELX_P
A
LEU
182
A
LEU
162
1
8
6
A
THR
183
A
THR
163
HELX_P
A
VAL
185
A
VAL
165
5
9
3
A
ASN
191
A
ASN
171
HELX_P
A
ALA
198
A
ALA
178
1
10
8
A
ASN
201
A
ASN
181
HELX_P
A
ALA
206
A
ALA
186
1
11
6
A
SER
229
A
SER
209
HELX_P
A
LEU
239
A
LEU
219
1
12
11
A
SER
241
A
SER
221
HELX_P
A
LYS
253
A
LYS
233
1
13
13
covale
1.349
both
A
ASP
186
A
C
ASP
166
1_555
A
MSE
187
A
N
MSE
167
1_555
covale
1.327
both
A
MSE
187
A
C
MSE
167
1_555
A
ALA
188
A
N
ALA
168
1_555
covale
1.348
both
A
ALA
231
A
C
ALA
211
1_555
A
MSE
232
A
N
MSE
212
1_555
covale
1.327
both
A
MSE
232
A
C
MSE
212
1_555
A
GLN
233
A
N
GLN
213
1_555
TRANSPORT PROTEIN
Periplasmic methionine binding protein, NLPA lipoprotein, PF03180 family, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, TRANSPORT PROTEIN
A
VAL
32
A
VAL
12
1
A
PRO
33
A
PRO
13
1.24
Q9HT68_PSEAE
UNP
1
22
Q9HT68
AESLTVAATPVPHAEILNVVKPLLAKEGVDLKIKEFTDYVQPNVQVSEKRLDANFFQHQPYLDEFNKAKGTDLVAVTGVH
IEPLGAYSSKYKKLDELPSGATVVIPNDATNGGRALLLLDKAGVIKLKDNKSITATPKDIVDNPKNIKIRELEAATLPRV
LTQVDMALINTNYALEAKLNPTKDALAIEGSDSPYVNILVARPDNKDSDAMQKLAKALHSAEIKQFIQEKYKGAVVPAF
22
260
4K3F
22
260
Q9HT68
A
1
2
240
1
expression tag
GLY
0
4K3F
A
Q9HT68
UNP
1
6
5
2
parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
parallel
anti-parallel
anti-parallel
anti-parallel
A
VAL
50
A
VAL
30
A
GLU
56
A
GLU
36
A
GLU
23
A
GLU
3
A
ALA
29
A
ALA
9
A
ALA
74
A
ALA
54
A
HIS
79
A
HIS
59
A
ASN
218
A
ASN
198
A
ALA
222
A
ALA
202
A
VAL
95
A
VAL
75
A
ILE
102
A
ILE
82
A
VAL
257
A
VAL
237
A
PRO
258
A
PRO
238
A
LYS
169
A
LYS
149
A
LEU
173
A
LEU
153
A
THR
123
A
THR
103
A
PRO
127
A
PRO
107
A
MSE
187
A
MSE
167
A
ILE
190
A
ILE
170
A
GLY
106
A
GLY
86
A
TYR
108
A
TYR
88
A
ALA
208
A
ALA
188
A
ILE
209
A
ILE
189
A
LYS
147
A
LYS
127
A
LEU
148
A
LEU
128
A
ILE
161
A
ILE
141
A
ASP
163
A
ASP
143
BINDING SITE FOR RESIDUE CL A 301
A
CL
301
Software
5
BINDING SITE FOR RESIDUE SO4 A 302
A
SO4
302
Software
8
BINDING SITE FOR RESIDUE SO4 A 303
A
SO4
303
Software
3
BINDING SITE FOR RESIDUE GOL A 304
A
GOL
304
Software
9
BINDING SITE FOR RESIDUE GOL A 305
A
GOL
305
Software
9
BINDING SITE FOR RESIDUE GOL A 306
A
GOL
306
Software
5
BINDING SITE FOR RESIDUE GOL A 307
A
GOL
307
Software
5
BINDING SITE FOR RESIDUE GOL A 308
A
GOL
308
Software
3
A
SER
68
A
SER
48
5
1_555
A
THR
92
A
THR
72
5
1_555
A
ASP
93
A
ASP
73
5
1_555
A
HOH
524
K
HOH
5
1_555
A
HOH
635
K
HOH
5
1_555
A
LYS
149
A
LYS
129
8
3_546
A
ASP
150
A
ASP
130
8
3_546
A
ARG
171
A
ARG
151
8
1_555
A
HOH
439
K
HOH
8
3_546
A
HOH
479
K
HOH
8
3_546
A
HOH
480
K
HOH
8
1_555
A
HOH
498
K
HOH
8
1_555
A
HOH
628
K
HOH
8
1_555
A
LYS
147
A
LYS
127
3
3_546
A
LYS
169
A
LYS
149
3
1_555
A
ARG
171
A
ARG
151
3
1_555
A
LYS
142
A
LYS
122
9
1_555
A
GLU
210
A
GLU
190
9
1_555
A
GLY
211
A
GLY
191
9
1_555
A
ASP
213
A
ASP
193
9
1_555
A
SER
214
A
SER
194
9
1_555
A
PRO
215
A
PRO
195
9
1_555
A
HOH
434
K
HOH
9
1_555
A
HOH
620
K
HOH
9
1_555
A
HOH
621
K
HOH
9
1_555
A
SER
24
A
SER
4
9
3_555
A
LEU
25
A
LEU
5
9
3_555
A
ASP
84
A
ASP
64
9
1_555
A
SER
229
A
SER
209
9
3_555
A
MSE
232
A
MSE
212
9
3_555
A
HOH
435
K
HOH
9
3_555
A
HOH
597
K
HOH
9
1_555
A
HOH
614
K
HOH
9
1_555
A
HOH
641
K
HOH
9
1_555
A
GLU
36
A
GLU
16
5
1_555
A
GLU
36
A
GLU
16
5
2_555
A
ASN
39
A
ASN
19
5
2_555
A
ASN
39
A
ASN
19
5
1_555
A
LYS
251
A
LYS
231
5
1_555
A
ASN
39
A
ASN
19
5
1_555
A
ILE
54
A
ILE
34
5
1_555
A
GLU
56
A
GLU
36
5
1_555
A
GLU
250
A
GLU
230
5
2_555
A
HOH
583
K
HOH
5
2_555
A
HIS
240
A
HIS
220
3
1_555
A
HOH
547
K
HOH
3
1_555
A
HOH
595
K
HOH
3
1_555
18
P 21 21 2