0.019135
0.000000
0.000000
0.000000
0.013096
0.000000
0.000000
0.000000
0.011666
0.00000
0.00000
0.00000
Sivaraman, J.
Iannuzzi, P.
Cygler, M.
Matte, A.
Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
52.261
76.362
85.717
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
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
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
335
87
101
10.1016/j.jmb.2003.10.003
14659742
Crystal structure of the RluD pseudouridine Synthase catalytic module, an
enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli
2003
100
1
IMAGE PLATE
2003-02-24
RIGAKU RAXIS HTC
GRAPHITE
MAD
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU MICROMAX-007
29229.068
Ribosomal large subunit pseudouridine synthase D
4.2.1.70
catalytic domain
1
man
polymer
18.015
water
294
nat
water
Pseudouridylate synthase; Uracil hydrolyase; suppressor of ftsH mutation
E.C.4.2.1.70
no
yes
ARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGL(MSE)VVAK
TVPAQTRLVESLQRREITREYEAVAIGH(MSE)TAGGTVDEPISRHPTKRTH(MSE)AVHP(MSE)GKPAVTHYRI
(MSE)EHFRVHTRLRLRLETGRTHQIRVH(MSE)AHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHAT
(MSE)LRLYHPISGIE(MSE)EWHAPIPQD(MSE)VELIEV(MSE)RADFEEHKDEVDWL
ARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPA
QTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTH
QIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVMRA
DFEEHKDEVDWL
A
RLUD_ECO57
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
Escherichia
Escherichia
sample
RLUD or SFHB
562
Escherichia coli
562
Escherichia coli
DL41
plasmid
1
2.64
53.0
microbatch under oil
7.
PEG 8000, KCL, Glycerol, pH 7., microbatch under oil, temperature 293K
293
Montreal-Kingston Bacterial Structural Genomics Initiative
BSGI
software
repository
Initial release
Version format compliance
Version format compliance
Refinement description
1
0
2003-11-04
1
1
2008-04-29
1
2
2011-07-13
1
3
2017-10-11
Y
RCSB
Y
RCSB
2003-06-20
REL
REL
HOH
water
HOH
327
2
HOH
HOH
327
A
HOH
328
2
HOH
HOH
328
A
HOH
329
2
HOH
HOH
329
A
HOH
330
2
HOH
HOH
330
A
HOH
331
2
HOH
HOH
331
A
HOH
332
2
HOH
HOH
332
A
HOH
333
2
HOH
HOH
333
A
HOH
334
2
HOH
HOH
334
A
HOH
335
2
HOH
HOH
335
A
HOH
336
2
HOH
HOH
336
A
HOH
337
2
HOH
HOH
337
A
HOH
338
2
HOH
HOH
338
A
HOH
339
2
HOH
HOH
339
A
HOH
340
2
HOH
HOH
340
A
HOH
341
2
HOH
HOH
341
A
HOH
342
2
HOH
HOH
342
A
HOH
343
2
HOH
HOH
343
A
HOH
344
2
HOH
HOH
344
A
HOH
345
2
HOH
HOH
345
A
HOH
346
2
HOH
HOH
346
A
HOH
347
2
HOH
HOH
347
A
HOH
348
2
HOH
HOH
348
A
HOH
349
2
HOH
HOH
349
A
HOH
350
2
HOH
HOH
350
A
HOH
351
2
HOH
HOH
351
A
HOH
352
2
HOH
HOH
352
A
HOH
353
2
HOH
HOH
353
A
HOH
354
2
HOH
HOH
354
A
HOH
355
2
HOH
HOH
355
A
HOH
356
2
HOH
HOH
356
A
HOH
357
2
HOH
HOH
357
A
HOH
358
2
HOH
HOH
358
A
HOH
359
2
HOH
HOH
359
A
HOH
360
2
HOH
HOH
360
A
HOH
361
2
HOH
HOH
361
A
HOH
362
2
HOH
HOH
362
A
HOH
363
2
HOH
HOH
363
A
HOH
364
2
HOH
HOH
364
A
HOH
365
2
HOH
HOH
365
A
HOH
366
2
HOH
HOH
366
A
HOH
367
2
HOH
HOH
367
A
HOH
368
2
HOH
HOH
368
A
HOH
369
2
HOH
HOH
369
A
HOH
370
2
HOH
HOH
370
A
HOH
371
2
HOH
HOH
371
A
HOH
372
2
HOH
HOH
372
A
HOH
373
2
HOH
HOH
373
A
HOH
374
2
HOH
HOH
374
A
HOH
375
2
HOH
HOH
375
A
HOH
376
2
HOH
HOH
376
A
HOH
377
2
HOH
HOH
377
A
HOH
378
2
HOH
HOH
378
A
HOH
379
2
HOH
HOH
379
A
HOH
380
2
HOH
HOH
380
A
HOH
381
2
HOH
HOH
381
A
HOH
382
2
HOH
HOH
382
A
HOH
383
2
HOH
HOH
383
A
HOH
384
2
HOH
HOH
384
A
HOH
385
2
HOH
HOH
385
A
HOH
386
2
HOH
HOH
386
A
HOH
387
2
HOH
HOH
387
A
HOH
388
2
HOH
HOH
388
A
HOH
389
2
HOH
HOH
389
A
HOH
390
2
HOH
HOH
390
A
HOH
391
2
HOH
HOH
391
A
HOH
392
2
HOH
HOH
392
A
HOH
393
2
HOH
HOH
393
A
HOH
394
2
HOH
HOH
394
A
HOH
395
2
HOH
HOH
395
A
HOH
396
2
HOH
HOH
396
A
HOH
397
2
HOH
HOH
397
A
HOH
398
2
HOH
HOH
398
A
HOH
399
2
HOH
HOH
399
A
HOH
400
2
HOH
HOH
400
A
HOH
401
2
HOH
HOH
401
A
HOH
402
2
HOH
HOH
402
A
HOH
403
2
HOH
HOH
403
A
HOH
404
2
HOH
HOH
404
A
HOH
405
2
HOH
HOH
405
A
HOH
406
2
HOH
HOH
406
A
HOH
407
2
HOH
HOH
407
A
HOH
408
2
HOH
HOH
408
A
HOH
409
2
HOH
HOH
409
A
HOH
410
2
HOH
HOH
410
A
HOH
411
2
HOH
HOH
411
A
HOH
412
2
HOH
HOH
412
A
HOH
413
2
HOH
HOH
413
A
HOH
414
2
HOH
HOH
414
A
HOH
415
2
HOH
HOH
415
A
HOH
416
2
HOH
HOH
416
A
HOH
417
2
HOH
HOH
417
A
HOH
418
2
HOH
HOH
418
A
HOH
419
2
HOH
HOH
419
A
HOH
420
2
HOH
HOH
420
A
HOH
421
2
HOH
HOH
421
A
HOH
422
2
HOH
HOH
422
A
HOH
423
2
HOH
HOH
423
A
HOH
424
2
HOH
HOH
424
A
HOH
425
2
HOH
HOH
425
A
HOH
426
2
HOH
HOH
426
A
HOH
427
2
HOH
HOH
427
A
HOH
428
2
HOH
HOH
428
A
HOH
429
2
HOH
HOH
429
A
HOH
430
2
HOH
HOH
430
A
HOH
431
2
HOH
HOH
431
A
HOH
432
2
HOH
HOH
432
A
HOH
433
2
HOH
HOH
433
A
HOH
434
2
HOH
HOH
434
A
HOH
435
2
HOH
HOH
435
A
HOH
436
2
HOH
HOH
436
A
HOH
437
2
HOH
HOH
437
A
HOH
438
2
HOH
HOH
438
A
HOH
439
2
HOH
HOH
439
A
HOH
440
2
HOH
HOH
440
A
HOH
441
2
HOH
HOH
441
A
HOH
442
2
HOH
HOH
442
A
HOH
443
2
HOH
HOH
443
A
HOH
444
2
HOH
HOH
444
A
HOH
445
2
HOH
HOH
445
A
HOH
446
2
HOH
HOH
446
A
HOH
447
2
HOH
HOH
447
A
HOH
448
2
HOH
HOH
448
A
HOH
449
2
HOH
HOH
449
A
HOH
450
2
HOH
HOH
450
A
HOH
451
2
HOH
HOH
451
A
HOH
452
2
HOH
HOH
452
A
HOH
453
2
HOH
HOH
453
A
HOH
454
2
HOH
HOH
454
A
HOH
455
2
HOH
HOH
455
A
HOH
456
2
HOH
HOH
456
A
HOH
457
2
HOH
HOH
457
A
HOH
458
2
HOH
HOH
458
A
HOH
459
2
HOH
HOH
459
A
HOH
460
2
HOH
HOH
460
A
HOH
461
2
HOH
HOH
461
A
HOH
462
2
HOH
HOH
462
A
HOH
463
2
HOH
HOH
463
A
HOH
464
2
HOH
HOH
464
A
HOH
465
2
HOH
HOH
465
A
HOH
466
2
HOH
HOH
466
A
HOH
467
2
HOH
HOH
467
A
HOH
468
2
HOH
HOH
468
A
HOH
469
2
HOH
HOH
469
A
HOH
470
2
HOH
HOH
470
A
HOH
471
2
HOH
HOH
471
A
HOH
472
2
HOH
HOH
472
A
HOH
473
2
HOH
HOH
473
A
HOH
474
2
HOH
HOH
474
A
HOH
475
2
HOH
HOH
475
A
HOH
476
2
HOH
HOH
476
A
HOH
477
2
HOH
HOH
477
A
HOH
478
2
HOH
HOH
478
A
HOH
479
2
HOH
HOH
479
A
HOH
480
2
HOH
HOH
480
A
HOH
481
2
HOH
HOH
481
A
HOH
482
2
HOH
HOH
482
A
HOH
483
2
HOH
HOH
483
A
HOH
484
2
HOH
HOH
484
A
HOH
485
2
HOH
HOH
485
A
HOH
486
2
HOH
HOH
486
A
HOH
487
2
HOH
HOH
487
A
HOH
488
2
HOH
HOH
488
A
HOH
489
2
HOH
HOH
489
A
HOH
490
2
HOH
HOH
490
A
HOH
491
2
HOH
HOH
491
A
HOH
492
2
HOH
HOH
492
A
HOH
493
2
HOH
HOH
493
A
HOH
494
2
HOH
HOH
494
A
HOH
495
2
HOH
HOH
495
A
HOH
496
2
HOH
HOH
496
A
HOH
497
2
HOH
HOH
497
A
HOH
498
2
HOH
HOH
498
A
HOH
499
2
HOH
HOH
499
A
HOH
500
2
HOH
HOH
500
A
HOH
501
2
HOH
HOH
501
A
HOH
502
2
HOH
HOH
502
A
HOH
503
2
HOH
HOH
503
A
HOH
504
2
HOH
HOH
504
A
HOH
505
2
HOH
HOH
505
A
HOH
506
2
HOH
HOH
506
A
HOH
507
2
HOH
HOH
507
A
HOH
508
2
HOH
HOH
508
A
HOH
509
2
HOH
HOH
509
A
HOH
510
2
HOH
HOH
510
A
HOH
511
2
HOH
HOH
511
A
HOH
512
2
HOH
HOH
512
A
HOH
513
2
HOH
HOH
513
A
HOH
514
2
HOH
HOH
514
A
HOH
515
2
HOH
HOH
515
A
HOH
516
2
HOH
HOH
516
A
HOH
517
2
HOH
HOH
517
A
HOH
518
2
HOH
HOH
518
A
HOH
519
2
HOH
HOH
519
A
HOH
520
2
HOH
HOH
520
A
HOH
521
2
HOH
HOH
521
A
HOH
522
2
HOH
HOH
522
A
HOH
523
2
HOH
HOH
523
A
HOH
524
2
HOH
HOH
524
A
HOH
525
2
HOH
HOH
525
A
HOH
526
2
HOH
HOH
526
A
HOH
527
2
HOH
HOH
527
A
HOH
528
2
HOH
HOH
528
A
HOH
529
2
HOH
HOH
529
A
HOH
530
2
HOH
HOH
530
A
HOH
531
2
HOH
HOH
531
A
HOH
532
2
HOH
HOH
532
A
HOH
533
2
HOH
HOH
533
A
HOH
534
2
HOH
HOH
534
A
HOH
535
2
HOH
HOH
535
A
HOH
536
2
HOH
HOH
536
A
HOH
537
2
HOH
HOH
537
A
HOH
538
2
HOH
HOH
538
A
HOH
539
2
HOH
HOH
539
A
HOH
540
2
HOH
HOH
540
A
HOH
541
2
HOH
HOH
541
A
HOH
542
2
HOH
HOH
542
A
HOH
543
2
HOH
HOH
543
A
HOH
544
2
HOH
HOH
544
A
HOH
545
2
HOH
HOH
545
A
HOH
546
2
HOH
HOH
546
A
HOH
547
2
HOH
HOH
547
A
HOH
548
2
HOH
HOH
548
A
HOH
549
2
HOH
HOH
549
A
HOH
550
2
HOH
HOH
550
A
HOH
551
2
HOH
HOH
551
A
HOH
552
2
HOH
HOH
552
A
HOH
553
2
HOH
HOH
553
A
HOH
554
2
HOH
HOH
554
A
HOH
555
2
HOH
HOH
555
A
HOH
556
2
HOH
HOH
556
A
HOH
557
2
HOH
HOH
557
A
HOH
558
2
HOH
HOH
558
A
HOH
559
2
HOH
HOH
559
A
HOH
560
2
HOH
HOH
560
A
HOH
561
2
HOH
HOH
561
A
HOH
562
2
HOH
HOH
562
A
HOH
563
2
HOH
HOH
563
A
HOH
564
2
HOH
HOH
564
A
HOH
565
2
HOH
HOH
565
A
HOH
566
2
HOH
HOH
566
A
HOH
567
2
HOH
HOH
567
A
HOH
568
2
HOH
HOH
568
A
HOH
569
2
HOH
HOH
569
A
HOH
570
2
HOH
HOH
570
A
HOH
571
2
HOH
HOH
571
A
HOH
572
2
HOH
HOH
572
A
HOH
573
2
HOH
HOH
573
A
HOH
574
2
HOH
HOH
574
A
HOH
575
2
HOH
HOH
575
A
HOH
576
2
HOH
HOH
576
A
HOH
577
2
HOH
HOH
577
A
HOH
578
2
HOH
HOH
578
A
HOH
579
2
HOH
HOH
579
A
HOH
580
2
HOH
HOH
580
A
HOH
581
2
HOH
HOH
581
A
HOH
582
2
HOH
HOH
582
A
HOH
583
2
HOH
HOH
583
A
HOH
584
2
HOH
HOH
584
A
HOH
585
2
HOH
HOH
585
A
HOH
586
2
HOH
HOH
586
A
HOH
587
2
HOH
HOH
587
A
HOH
588
2
HOH
HOH
588
A
HOH
589
2
HOH
HOH
589
A
HOH
590
2
HOH
HOH
590
A
HOH
591
2
HOH
HOH
591
A
HOH
592
2
HOH
HOH
592
A
HOH
593
2
HOH
HOH
593
A
HOH
594
2
HOH
HOH
594
A
HOH
595
2
HOH
HOH
595
A
HOH
596
2
HOH
HOH
596
A
HOH
597
2
HOH
HOH
597
A
HOH
598
2
HOH
HOH
598
A
HOH
599
2
HOH
HOH
599
A
HOH
600
2
HOH
HOH
600
A
HOH
601
2
HOH
HOH
601
A
HOH
602
2
HOH
HOH
602
A
HOH
603
2
HOH
HOH
603
A
HOH
604
2
HOH
HOH
604
A
HOH
605
2
HOH
HOH
605
A
HOH
606
2
HOH
HOH
606
A
HOH
607
2
HOH
HOH
607
A
HOH
608
2
HOH
HOH
608
A
HOH
609
2
HOH
HOH
609
A
HOH
610
2
HOH
HOH
610
A
HOH
611
2
HOH
HOH
611
A
HOH
612
2
HOH
HOH
612
A
HOH
613
2
HOH
HOH
613
A
HOH
614
2
HOH
HOH
614
A
HOH
615
2
HOH
HOH
615
A
HOH
616
2
HOH
HOH
616
A
HOH
617
2
HOH
HOH
617
A
HOH
618
2
HOH
HOH
618
A
HOH
619
2
HOH
HOH
619
A
HOH
620
2
HOH
HOH
620
A
ALA
75
n
1
ALA
75
A
ARG
76
n
2
ARG
76
A
PHE
77
n
3
PHE
77
A
GLU
78
n
4
GLU
78
A
PRO
79
n
5
PRO
79
A
GLN
80
n
6
GLN
80
A
ASP
81
n
7
ASP
81
A
ILE
82
n
8
ILE
82
A
PRO
83
n
9
PRO
83
A
LEU
84
n
10
LEU
84
A
ASP
85
n
11
ASP
85
A
ILE
86
n
12
ILE
86
A
VAL
87
n
13
VAL
87
A
TYR
88
n
14
TYR
88
A
GLU
89
n
15
GLU
89
A
ASP
90
n
16
ASP
90
A
GLU
91
n
17
GLU
91
A
ASP
92
n
18
ASP
92
A
ILE
93
n
19
ILE
93
A
ILE
94
n
20
ILE
94
A
VAL
95
n
21
VAL
95
A
ILE
96
n
22
ILE
96
A
ASN
97
n
23
ASN
97
A
LYS
98
n
24
LYS
98
A
PRO
99
n
25
PRO
99
A
ARG
100
n
26
ARG
100
A
ASP
101
n
27
ASP
101
A
LEU
102
n
28
LEU
102
A
VAL
103
n
29
VAL
103
A
VAL
104
n
30
VAL
104
A
HIS
105
n
31
HIS
105
A
PRO
106
n
32
PRO
106
A
GLY
107
n
33
GLY
107
A
ALA
108
n
34
ALA
108
A
GLY
109
n
35
GLY
109
A
ASN
110
n
36
ASN
110
A
PRO
111
n
37
PRO
111
A
ASP
112
n
38
ASP
112
A
GLY
113
n
39
GLY
113
A
THR
114
n
40
THR
114
A
VAL
115
n
41
VAL
115
A
LEU
116
n
42
LEU
116
A
ASN
117
n
43
ASN
117
A
ALA
118
n
44
ALA
118
A
LEU
119
n
45
LEU
119
A
LEU
120
n
46
LEU
120
A
HIS
121
n
47
HIS
121
A
TYR
122
n
48
TYR
122
A
TYR
123
n
49
TYR
123
A
PRO
124
n
50
PRO
124
A
PRO
125
n
51
PRO
125
A
ILE
126
n
52
ILE
126
A
ALA
127
n
53
ALA
127
A
ASP
128
n
54
ASP
128
A
VAL
129
n
55
VAL
129
A
PRO
130
n
56
PRO
130
A
ARG
131
n
57
ARG
131
A
ALA
132
n
58
ALA
132
A
GLY
133
n
59
GLY
133
A
ILE
134
n
60
ILE
134
A
VAL
135
n
61
VAL
135
A
HIS
136
n
62
HIS
136
A
ARG
137
n
63
ARG
137
A
LEU
138
n
64
LEU
138
A
ASP
139
n
65
ASP
139
A
LYS
140
n
66
LYS
140
A
ASP
141
n
67
ASP
141
A
THR
142
n
68
THR
142
A
THR
143
n
69
THR
143
A
GLY
144
n
70
GLY
144
A
LEU
145
n
71
LEU
145
A
MSE
146
n
72
MSE
146
A
VAL
147
n
73
VAL
147
A
VAL
148
n
74
VAL
148
A
ALA
149
n
75
ALA
149
A
LYS
150
n
76
LYS
150
A
THR
151
n
77
THR
151
A
VAL
152
n
78
VAL
152
A
PRO
153
n
79
PRO
153
A
ALA
154
n
80
ALA
154
A
GLN
155
n
81
GLN
155
A
THR
156
n
82
THR
156
A
ARG
157
n
83
ARG
157
A
LEU
158
n
84
LEU
158
A
VAL
159
n
85
VAL
159
A
GLU
160
n
86
GLU
160
A
SER
161
n
87
SER
161
A
LEU
162
n
88
LEU
162
A
GLN
163
n
89
GLN
163
A
ARG
164
n
90
ARG
164
A
ARG
165
n
91
ARG
165
A
GLU
166
n
92
GLU
166
A
ILE
167
n
93
ILE
167
A
THR
168
n
94
THR
168
A
ARG
169
n
95
ARG
169
A
GLU
170
n
96
GLU
170
A
TYR
171
n
97
TYR
171
A
GLU
172
n
98
GLU
172
A
ALA
173
n
99
ALA
173
A
VAL
174
n
100
VAL
174
A
ALA
175
n
101
ALA
175
A
ILE
176
n
102
ILE
176
A
GLY
177
n
103
GLY
177
A
HIS
178
n
104
HIS
178
A
MSE
179
n
105
MSE
179
A
THR
180
n
106
THR
180
A
ALA
181
n
107
ALA
181
A
GLY
182
n
108
GLY
182
A
GLY
183
n
109
GLY
183
A
THR
184
n
110
THR
184
A
VAL
185
n
111
VAL
185
A
ASP
186
n
112
ASP
186
A
GLU
187
n
113
GLU
187
A
PRO
188
n
114
PRO
188
A
ILE
189
n
115
ILE
189
A
SER
190
n
116
SER
190
A
ARG
191
n
117
ARG
191
A
HIS
192
n
118
HIS
192
A
PRO
193
n
119
PRO
193
A
THR
194
n
120
THR
194
A
LYS
195
n
121
LYS
195
A
ARG
196
n
122
ARG
196
A
THR
197
n
123
THR
197
A
HIS
198
n
124
HIS
198
A
MSE
199
n
125
MSE
199
A
ALA
200
n
126
ALA
200
A
VAL
201
n
127
VAL
201
A
HIS
202
n
128
HIS
202
A
PRO
203
n
129
PRO
203
A
MSE
204
n
130
MSE
204
A
GLY
205
n
131
GLY
205
A
LYS
206
n
132
LYS
206
A
PRO
207
n
133
PRO
207
A
ALA
208
n
134
ALA
208
A
VAL
209
n
135
VAL
209
A
THR
210
n
136
THR
210
A
HIS
211
n
137
HIS
211
A
TYR
212
n
138
TYR
212
A
ARG
213
n
139
ARG
213
A
ILE
214
n
140
ILE
214
A
MSE
215
n
141
MSE
215
A
GLU
216
n
142
GLU
216
A
HIS
217
n
143
HIS
217
A
PHE
218
n
144
PHE
218
A
ARG
219
n
145
ARG
219
A
VAL
220
n
146
VAL
220
A
HIS
221
n
147
HIS
221
A
THR
222
n
148
THR
222
A
ARG
223
n
149
ARG
223
A
LEU
224
n
150
LEU
224
A
ARG
225
n
151
ARG
225
A
LEU
226
n
152
LEU
226
A
ARG
227
n
153
ARG
227
A
LEU
228
n
154
LEU
228
A
GLU
229
n
155
GLU
229
A
THR
230
n
156
THR
230
A
GLY
231
n
157
GLY
231
A
ARG
232
n
158
ARG
232
A
THR
233
n
159
THR
233
A
HIS
234
n
160
HIS
234
A
GLN
235
n
161
GLN
235
A
ILE
236
n
162
ILE
236
A
ARG
237
n
163
ARG
237
A
VAL
238
n
164
VAL
238
A
HIS
239
n
165
HIS
239
A
MSE
240
n
166
MSE
240
A
ALA
241
n
167
ALA
241
A
HIS
242
n
168
HIS
242
A
ILE
243
n
169
ILE
243
A
THR
244
n
170
THR
244
A
HIS
245
n
171
HIS
245
A
PRO
246
n
172
PRO
246
A
LEU
247
n
173
LEU
247
A
VAL
248
n
174
VAL
248
A
GLY
249
n
175
GLY
249
A
ASP
250
n
176
ASP
250
A
PRO
251
n
177
PRO
251
A
VAL
252
n
178
VAL
252
A
TYR
253
n
179
TYR
253
A
GLY
254
n
180
GLY
254
A
GLY
255
n
181
GLY
255
A
ARG
256
n
182
ARG
256
A
PRO
257
n
183
PRO
257
A
ARG
258
n
184
ARG
258
A
PRO
259
n
185
PRO
259
A
PRO
260
n
186
PRO
260
A
LYS
261
n
187
LYS
261
A
GLY
262
n
188
GLY
262
A
ALA
263
n
189
ALA
263
A
SER
264
n
190
SER
264
A
GLU
265
n
191
GLU
265
A
ALA
266
n
192
ALA
266
A
PHE
267
n
193
PHE
267
A
ILE
268
n
194
ILE
268
A
SER
269
n
195
SER
269
A
THR
270
n
196
THR
270
A
LEU
271
n
197
LEU
271
A
ARG
272
n
198
ARG
272
A
LYS
273
n
199
LYS
273
A
PHE
274
n
200
PHE
274
A
ASP
275
n
201
ASP
275
A
ARG
276
n
202
ARG
276
A
GLN
277
n
203
GLN
277
A
ALA
278
n
204
ALA
278
A
LEU
279
n
205
LEU
279
A
HIS
280
n
206
HIS
280
A
ALA
281
n
207
ALA
281
A
THR
282
n
208
THR
282
A
MSE
283
n
209
MSE
283
A
LEU
284
n
210
LEU
284
A
ARG
285
n
211
ARG
285
A
LEU
286
n
212
LEU
286
A
TYR
287
n
213
TYR
287
A
HIS
288
n
214
HIS
288
A
PRO
289
n
215
PRO
289
A
ILE
290
n
216
ILE
290
A
SER
291
n
217
SER
291
A
GLY
292
n
218
GLY
292
A
ILE
293
n
219
ILE
293
A
GLU
294
n
220
GLU
294
A
MSE
295
n
221
MSE
295
A
GLU
296
n
222
GLU
296
A
TRP
297
n
223
TRP
297
A
HIS
298
n
224
HIS
298
A
ALA
299
n
225
ALA
299
A
PRO
300
n
226
PRO
300
A
ILE
301
n
227
ILE
301
A
PRO
302
n
228
PRO
302
A
GLN
303
n
229
GLN
303
A
ASP
304
n
230
ASP
304
A
MSE
305
n
231
MSE
305
A
VAL
306
n
232
VAL
306
A
GLU
307
n
233
GLU
307
A
LEU
308
n
234
LEU
308
A
ILE
309
n
235
ILE
309
A
GLU
310
n
236
GLU
310
A
VAL
311
n
237
VAL
311
A
MSE
312
n
238
MSE
312
A
ARG
313
n
239
ARG
313
A
ALA
314
n
240
ALA
314
A
ASP
315
n
241
ASP
315
A
PHE
316
n
242
PHE
316
A
GLU
317
n
243
GLU
317
A
GLU
318
n
244
GLU
318
A
HIS
319
n
245
HIS
319
A
LYS
320
n
246
LYS
320
A
ASP
321
n
247
ASP
321
A
GLU
322
n
248
GLU
322
A
VAL
323
n
249
VAL
323
A
ASP
324
n
250
ASP
324
A
TRP
325
n
251
TRP
325
A
LEU
326
n
252
LEU
326
A
author_defined_assembly
1
monomeric
A
MSE
146
SELENOMETHIONINE
A
MSE
72
MET
A
MSE
179
SELENOMETHIONINE
A
MSE
105
MET
A
MSE
199
SELENOMETHIONINE
A
MSE
125
MET
A
MSE
204
SELENOMETHIONINE
A
MSE
130
MET
A
MSE
215
SELENOMETHIONINE
A
MSE
141
MET
A
MSE
240
SELENOMETHIONINE
A
MSE
166
MET
A
MSE
283
SELENOMETHIONINE
A
MSE
209
MET
A
MSE
295
SELENOMETHIONINE
A
MSE
221
MET
A
MSE
305
SELENOMETHIONINE
A
MSE
231
MET
A
MSE
312
SELENOMETHIONINE
A
MSE
238
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
N
TYR
88
A
N
TYR
14
A
O
VAL
95
A
O
VAL
21
A
N
ILE
94
A
N
ILE
20
A
O
VAL
148
A
O
VAL
74
A
N
THR
143
A
N
THR
69
A
O
ALA
281
A
O
ALA
207
A
O
MSE
283
A
O
MSE
209
A
N
GLU
170
A
N
GLU
96
A
N
ALA
173
A
N
ALA
99
A
O
LEU
224
A
O
LEU
150
A
O
ARG
223
A
O
ARG
149
A
N
GLU
216
A
N
GLU
142
A
O
TYR
212
A
O
TYR
138
A
N
GLY
183
A
N
GLY
109
A
N
TYR
88
A
N
TYR
14
A
O
VAL
95
A
O
VAL
21
A
N
ILE
94
A
N
ILE
20
A
O
VAL
148
A
O
VAL
74
A
N
THR
143
A
N
THR
69
A
O
ALA
281
A
O
ALA
207
A
N
LEU
286
A
N
LEU
212
A
O
MSE
295
A
O
MSE
221
A
N
SER
190
A
N
SER
116
A
O
ALA
200
A
O
ALA
126
1
-3.75
0.50
120.30
116.55
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
237
237
237
N
1
A
ARG
76
-18.61
-80.96
1
A
THR
244
87.54
7.94
0.243
0.218
1.80
50.
2406
32444
29910
8.0
RANDAM
1
0
0
MAD
Engh & Huber
0.29
1.80
50.
294
2315
0
0
2021
0.01
1.8
1.80
50.
1PRZ
32444
32444
-3
0.065
1
12.4
99.4
1.80
1.86
98.3
data collection
CRYSATL
CLEAR
data reduction
HKL-2000
phasing
SOLVE
refinement
CNS
data reduction
CrystalClear
(MSC/RIGAKU)
data scaling
HKL-2000
Ribosomal large subunit pseudouridine synthase D (E.C.4.2.1.70)
Crystal structure of pseudouridine synthase RluD catalytic module
1
N
N
2
N
N
A
THR
114
A
THR
40
HELX_P
A
TYR
123
A
TYR
49
1
1
10
A
PRO
124
A
PRO
50
HELX_P
A
ILE
134
A
ILE
60
5
2
11
A
THR
151
A
THR
77
HELX_P
A
ARG
164
A
ARG
90
1
3
14
A
HIS
234
A
HIS
160
HELX_P
A
ILE
243
A
ILE
169
1
4
10
A
SER
264
A
SER
190
HELX_P
A
PHE
274
A
PHE
200
1
5
11
A
PRO
302
A
PRO
228
HELX_P
A
HIS
319
A
HIS
245
1
6
18
covale
1.331
A
LEU
145
A
C
LEU
71
1_555
A
MSE
146
A
N
MSE
72
1_555
covale
1.328
A
MSE
146
A
C
MSE
72
1_555
A
VAL
147
A
N
VAL
73
1_555
covale
1.322
A
HIS
178
A
C
HIS
104
1_555
A
MSE
179
A
N
MSE
105
1_555
covale
1.321
A
MSE
179
A
C
MSE
105
1_555
A
THR
180
A
N
THR
106
1_555
covale
1.331
A
HIS
198
A
C
HIS
124
1_555
A
MSE
199
A
N
MSE
125
1_555
covale
1.325
A
MSE
199
A
C
MSE
125
1_555
A
ALA
200
A
N
ALA
126
1_555
covale
1.328
A
PRO
203
A
C
PRO
129
1_555
A
MSE
204
A
N
MSE
130
1_555
covale
1.331
A
MSE
204
A
C
MSE
130
1_555
A
GLY
205
A
N
GLY
131
1_555
covale
1.327
A
ILE
214
A
C
ILE
140
1_555
A
MSE
215
A
N
MSE
141
1_555
covale
1.323
A
MSE
215
A
C
MSE
141
1_555
A
GLU
216
A
N
GLU
142
1_555
covale
1.339
A
HIS
239
A
C
HIS
165
1_555
A
MSE
240
A
N
MSE
166
1_555
covale
1.325
A
MSE
240
A
C
MSE
166
1_555
A
ALA
241
A
N
ALA
167
1_555
covale
1.326
A
THR
282
A
C
THR
208
1_555
A
MSE
283
A
N
MSE
209
1_555
covale
1.326
A
MSE
283
A
C
MSE
209
1_555
A
LEU
284
A
N
LEU
210
1_555
covale
1.326
A
GLU
294
A
C
GLU
220
1_555
A
MSE
295
A
N
MSE
221
1_555
covale
1.322
A
MSE
295
A
C
MSE
221
1_555
A
GLU
296
A
N
GLU
222
1_555
covale
1.332
A
ASP
304
A
C
ASP
230
1_555
A
MSE
305
A
N
MSE
231
1_555
covale
1.326
A
MSE
305
A
C
MSE
231
1_555
A
VAL
306
A
N
VAL
232
1_555
covale
1.336
A
VAL
311
A
C
VAL
237
1_555
A
MSE
312
A
N
MSE
238
1_555
covale
1.325
A
MSE
312
A
C
MSE
238
1_555
A
ARG
313
A
N
ARG
239
1_555
LYASE
Pseudouridine synthase, RluD, Montreal-Kingston Bacterial Structural Genomics Initiative, BSGI, Structural Genomics, LYASE
RLUD_ECO57
UNP
1
75
Q8X9F0
ARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPA
QTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTH
QIRVHMAHITHPLVGDPVYGGRPRPPKGASEAFISTLRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEVMRA
DFEEHKDEVDWL
75
326
1PRZ
75
326
Q8X9F0
A
1
1
252
1
MET
MODIFIED RESIDUE
MSE
146
1PRZ
A
Q8X9F0
UNP
146
72
1
MET
MODIFIED RESIDUE
MSE
179
1PRZ
A
Q8X9F0
UNP
179
105
1
MET
MODIFIED RESIDUE
MSE
199
1PRZ
A
Q8X9F0
UNP
199
125
1
MET
MODIFIED RESIDUE
MSE
204
1PRZ
A
Q8X9F0
UNP
204
130
1
MET
MODIFIED RESIDUE
MSE
215
1PRZ
A
Q8X9F0
UNP
215
141
1
MET
MODIFIED RESIDUE
MSE
240
1PRZ
A
Q8X9F0
UNP
240
166
1
MET
MODIFIED RESIDUE
MSE
283
1PRZ
A
Q8X9F0
UNP
283
209
1
MET
MODIFIED RESIDUE
MSE
295
1PRZ
A
Q8X9F0
UNP
295
221
1
MET
MODIFIED RESIDUE
MSE
305
1PRZ
A
Q8X9F0
UNP
305
231
1
MET
MODIFIED RESIDUE
MSE
312
1PRZ
A
Q8X9F0
UNP
312
238
8
5
2
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
ILE
86
A
ILE
12
A
GLU
89
A
GLU
15
A
ILE
93
A
ILE
19
A
LYS
98
A
LYS
24
A
THR
143
A
THR
69
A
ALA
149
A
ALA
75
A
LEU
279
A
LEU
205
A
TYR
287
A
TYR
213
A
THR
168
A
THR
94
A
ILE
176
A
ILE
102
A
HIS
221
A
HIS
147
A
LEU
228
A
LEU
154
A
VAL
209
A
VAL
135
A
HIS
217
A
HIS
143
A
GLY
183
A
GLY
109
A
ASP
186
A
ASP
112
A
ILE
86
A
ILE
12
A
GLU
89
A
GLU
15
A
ILE
93
A
ILE
19
A
LYS
98
A
LYS
24
A
THR
143
A
THR
69
A
ALA
149
A
ALA
75
A
LEU
279
A
LEU
205
A
TYR
287
A
TYR
213
A
GLU
294
A
GLU
220
A
HIS
298
A
HIS
224
A
ILE
189
A
ILE
115
A
ARG
191
A
ARG
117
A
MSE
199
A
MSE
125
A
VAL
201
A
VAL
127
19
orthorhombic
P 21 21 21