0.014269
0.008238
0.000000
0.000000
0.016476
0.000000
0.000000
0.000000
0.010505
0.00000
0.00000
0.00000
Thomas, S.R.
LaRonde-LeBlanc, N.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
70.083
70.083
95.190
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
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C14 H20 N6 O5 S
384.411
n
S-ADENOSYL-L-HOMOCYSTEINE
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
Nucleic Acids Res.
NARHAD
0389
0305-1048
39
2445
2457
10.1093/nar/gkq1131
21087996
Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis.
2011
100
1
CCD
2007-02-15
ADSC QUANTUM 315
KOHZU HLD8-24
SINGLE WAVELENGTH
x-ray
1
.99998
1.0
24-ID-C
APS
.99998
SYNCHROTRON
APS BEAMLINE 24-ID-C
28382.510
Ribosome biogenesis Nep1 RNA methyltransferase
1
man
polymer
181.189
TYROSINE
1
syn
non-polymer
384.411
S-ADENOSYL-L-HOMOCYSTEINE
1
syn
non-polymer
18.015
water
240
nat
water
no
no
HHHHHHRSDITSLYKKVGENLYFQGMGSAFVFLEASLELIPQKIRGHPAVRADAIRRGKRPEKILLDDSKHHTAMKSLEF
REKRGRPDIVHQCLLLLLDSPLRDFEVYVHTLNGEIIWVNRETRLPRNYNRFVGLMEKLFEERRITAGDTTLIEFKDVGL
RDIVRGRDVLLFREKGGRFEFSELLDGDVAVCIGAFPHGDFFEETLRELGEFKEVSLGTESYTSLYVTSRVLCEYERVRA
HKVG
HHHHHHRSDITSLYKKVGENLYFQGMGSAFVFLEASLELIPQKIRGHPAVRADAIRRGKRPEKILLDDSKHHTAMKSLEF
REKRGRPDIVHQCLLLLLDSPLRDFEVYVHTLNGEIIWVNRETRLPRNYNRFVGLMEKLFEERRITAGDTTLIEFKDVGL
RDIVRGRDVLLFREKGGRFEFSELLDGDVAVCIGAFPHGDFFEETLRELGEFKEVSLGTESYTSLYVTSRVLCEYERVRA
HKVG
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
sample
AF_0734
2234
Archaeoglobus fulgidus
511693
Escherichia coli
BL21
plasmid
pdest527
1
2.38
48.27
3-4M NaCl, 0.1M HEPES, pH 7.0-8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
7.0-8.0
293
pdbx_unobs_or_zero_occ_atoms
software
repository
Initial release
Version format compliance
Advisory
Refinement description
1
0
2011-01-19
1
1
2011-07-13
1
2
2017-11-08
RCSB
Y
RCSB
2010-07-30
REL
REL
TYR
TYROSINE
SAH
S-ADENOSYL-L-HOMOCYSTEINE
HOH
water
TYR
220
2
TYR
TYR
220
A
SAH
301
3
SAH
SAH
301
A
HOH
221
4
HOH
HOH
221
A
HOH
222
4
HOH
HOH
222
A
HOH
223
4
HOH
HOH
223
A
HOH
224
4
HOH
HOH
224
A
HOH
225
4
HOH
HOH
225
A
HOH
226
4
HOH
HOH
226
A
HOH
227
4
HOH
HOH
227
A
HOH
228
4
HOH
HOH
228
A
HOH
229
4
HOH
HOH
229
A
HOH
230
4
HOH
HOH
230
A
HOH
231
4
HOH
HOH
231
A
HOH
232
4
HOH
HOH
232
A
HOH
233
4
HOH
HOH
233
A
HOH
234
4
HOH
HOH
234
A
HOH
235
4
HOH
HOH
235
A
HOH
236
4
HOH
HOH
236
A
HOH
237
4
HOH
HOH
237
A
HOH
238
4
HOH
HOH
238
A
HOH
239
4
HOH
HOH
239
A
HOH
240
4
HOH
HOH
240
A
HOH
241
4
HOH
HOH
241
A
HOH
242
4
HOH
HOH
242
A
HOH
243
4
HOH
HOH
243
A
HOH
244
4
HOH
HOH
244
A
HOH
245
4
HOH
HOH
245
A
HOH
246
4
HOH
HOH
246
A
HOH
247
4
HOH
HOH
247
A
HOH
248
4
HOH
HOH
248
A
HOH
249
4
HOH
HOH
249
A
HOH
250
4
HOH
HOH
250
A
HOH
251
4
HOH
HOH
251
A
HOH
252
4
HOH
HOH
252
A
HOH
253
4
HOH
HOH
253
A
HOH
254
4
HOH
HOH
254
A
HOH
255
4
HOH
HOH
255
A
HOH
256
4
HOH
HOH
256
A
HOH
257
4
HOH
HOH
257
A
HOH
258
4
HOH
HOH
258
A
HOH
259
4
HOH
HOH
259
A
HOH
260
4
HOH
HOH
260
A
HOH
261
4
HOH
HOH
261
A
HOH
262
4
HOH
HOH
262
A
HOH
263
4
HOH
HOH
263
A
HOH
264
4
HOH
HOH
264
A
HOH
265
4
HOH
HOH
265
A
HOH
266
4
HOH
HOH
266
A
HOH
267
4
HOH
HOH
267
A
HOH
268
4
HOH
HOH
268
A
HOH
269
4
HOH
HOH
269
A
HOH
270
4
HOH
HOH
270
A
HOH
271
4
HOH
HOH
271
A
HOH
272
4
HOH
HOH
272
A
HOH
273
4
HOH
HOH
273
A
HOH
274
4
HOH
HOH
274
A
HOH
275
4
HOH
HOH
275
A
HOH
276
4
HOH
HOH
276
A
HOH
277
4
HOH
HOH
277
A
HOH
278
4
HOH
HOH
278
A
HOH
279
4
HOH
HOH
279
A
HOH
280
4
HOH
HOH
280
A
HOH
281
4
HOH
HOH
281
A
HOH
282
4
HOH
HOH
282
A
HOH
283
4
HOH
HOH
283
A
HOH
284
4
HOH
HOH
284
A
HOH
285
4
HOH
HOH
285
A
HOH
286
4
HOH
HOH
286
A
HOH
287
4
HOH
HOH
287
A
HOH
288
4
HOH
HOH
288
A
HOH
289
4
HOH
HOH
289
A
HOH
290
4
HOH
HOH
290
A
HOH
291
4
HOH
HOH
291
A
HOH
292
4
HOH
HOH
292
A
HOH
293
4
HOH
HOH
293
A
HOH
294
4
HOH
HOH
294
A
HOH
295
4
HOH
HOH
295
A
HOH
296
4
HOH
HOH
296
A
HOH
297
4
HOH
HOH
297
A
HOH
298
4
HOH
HOH
298
A
HOH
299
4
HOH
HOH
299
A
HOH
300
4
HOH
HOH
300
A
HOH
302
4
HOH
HOH
302
A
HOH
303
4
HOH
HOH
303
A
HOH
304
4
HOH
HOH
304
A
HOH
305
4
HOH
HOH
305
A
HOH
306
4
HOH
HOH
306
A
HOH
307
4
HOH
HOH
307
A
HOH
308
4
HOH
HOH
308
A
HOH
309
4
HOH
HOH
309
A
HOH
310
4
HOH
HOH
310
A
HOH
311
4
HOH
HOH
311
A
HOH
312
4
HOH
HOH
312
A
HOH
313
4
HOH
HOH
313
A
HOH
314
4
HOH
HOH
314
A
HOH
315
4
HOH
HOH
315
A
HOH
316
4
HOH
HOH
316
A
HOH
317
4
HOH
HOH
317
A
HOH
318
4
HOH
HOH
318
A
HOH
319
4
HOH
HOH
319
A
HOH
320
4
HOH
HOH
320
A
HOH
321
4
HOH
HOH
321
A
HOH
322
4
HOH
HOH
322
A
HOH
323
4
HOH
HOH
323
A
HOH
324
4
HOH
HOH
324
A
HOH
325
4
HOH
HOH
325
A
HOH
326
4
HOH
HOH
326
A
HOH
327
4
HOH
HOH
327
A
HOH
328
4
HOH
HOH
328
A
HOH
329
4
HOH
HOH
329
A
HOH
330
4
HOH
HOH
330
A
HOH
331
4
HOH
HOH
331
A
HOH
332
4
HOH
HOH
332
A
HOH
333
4
HOH
HOH
333
A
HOH
334
4
HOH
HOH
334
A
HOH
335
4
HOH
HOH
335
A
HOH
336
4
HOH
HOH
336
A
HOH
337
4
HOH
HOH
337
A
HOH
338
4
HOH
HOH
338
A
HOH
339
4
HOH
HOH
339
A
HOH
340
4
HOH
HOH
340
A
HOH
341
4
HOH
HOH
341
A
HOH
342
4
HOH
HOH
342
A
HOH
343
4
HOH
HOH
343
A
HOH
344
4
HOH
HOH
344
A
HOH
345
4
HOH
HOH
345
A
HOH
346
4
HOH
HOH
346
A
HOH
347
4
HOH
HOH
347
A
HOH
348
4
HOH
HOH
348
A
HOH
349
4
HOH
HOH
349
A
HOH
350
4
HOH
HOH
350
A
HOH
351
4
HOH
HOH
351
A
HOH
352
4
HOH
HOH
352
A
HOH
353
4
HOH
HOH
353
A
HOH
354
4
HOH
HOH
354
A
HOH
355
4
HOH
HOH
355
A
HOH
356
4
HOH
HOH
356
A
HOH
357
4
HOH
HOH
357
A
HOH
358
4
HOH
HOH
358
A
HOH
359
4
HOH
HOH
359
A
HOH
360
4
HOH
HOH
360
A
HOH
361
4
HOH
HOH
361
A
HOH
362
4
HOH
HOH
362
A
HOH
363
4
HOH
HOH
363
A
HOH
364
4
HOH
HOH
364
A
HOH
365
4
HOH
HOH
365
A
HOH
366
4
HOH
HOH
366
A
HOH
367
4
HOH
HOH
367
A
HOH
368
4
HOH
HOH
368
A
HOH
369
4
HOH
HOH
369
A
HOH
370
4
HOH
HOH
370
A
HOH
371
4
HOH
HOH
371
A
HOH
372
4
HOH
HOH
372
A
HOH
373
4
HOH
HOH
373
A
HOH
374
4
HOH
HOH
374
A
HOH
375
4
HOH
HOH
375
A
HOH
376
4
HOH
HOH
376
A
HOH
377
4
HOH
HOH
377
A
HOH
378
4
HOH
HOH
378
A
HOH
379
4
HOH
HOH
379
A
HOH
380
4
HOH
HOH
380
A
HOH
381
4
HOH
HOH
381
A
HOH
382
4
HOH
HOH
382
A
HOH
383
4
HOH
HOH
383
A
HOH
384
4
HOH
HOH
384
A
HOH
385
4
HOH
HOH
385
A
HOH
386
4
HOH
HOH
386
A
HOH
387
4
HOH
HOH
387
A
HOH
388
4
HOH
HOH
388
A
HOH
389
4
HOH
HOH
389
A
HOH
390
4
HOH
HOH
390
A
HOH
391
4
HOH
HOH
391
A
HOH
392
4
HOH
HOH
392
A
HOH
393
4
HOH
HOH
393
A
HOH
394
4
HOH
HOH
394
A
HOH
395
4
HOH
HOH
395
A
HOH
396
4
HOH
HOH
396
A
HOH
397
4
HOH
HOH
397
A
HOH
398
4
HOH
HOH
398
A
HOH
399
4
HOH
HOH
399
A
HOH
400
4
HOH
HOH
400
A
HOH
401
4
HOH
HOH
401
A
HOH
402
4
HOH
HOH
402
A
HOH
403
4
HOH
HOH
403
A
HOH
404
4
HOH
HOH
404
A
HOH
405
4
HOH
HOH
405
A
HOH
406
4
HOH
HOH
406
A
HOH
407
4
HOH
HOH
407
A
HOH
408
4
HOH
HOH
408
A
HOH
409
4
HOH
HOH
409
A
HOH
410
4
HOH
HOH
410
A
HOH
411
4
HOH
HOH
411
A
HOH
412
4
HOH
HOH
412
A
HOH
413
4
HOH
HOH
413
A
HOH
414
4
HOH
HOH
414
A
HOH
415
4
HOH
HOH
415
A
HOH
416
4
HOH
HOH
416
A
HOH
417
4
HOH
HOH
417
A
HOH
418
4
HOH
HOH
418
A
HOH
419
4
HOH
HOH
419
A
HOH
420
4
HOH
HOH
420
A
HOH
421
4
HOH
HOH
421
A
HOH
422
4
HOH
HOH
422
A
HOH
423
4
HOH
HOH
423
A
HOH
424
4
HOH
HOH
424
A
HOH
425
4
HOH
HOH
425
A
HOH
426
4
HOH
HOH
426
A
HOH
427
4
HOH
HOH
427
A
HOH
428
4
HOH
HOH
428
A
HOH
429
4
HOH
HOH
429
A
HOH
430
4
HOH
HOH
430
A
HOH
431
4
HOH
HOH
431
A
HOH
432
4
HOH
HOH
432
A
HOH
433
4
HOH
HOH
433
A
HOH
434
4
HOH
HOH
434
A
HOH
435
4
HOH
HOH
435
A
HOH
436
4
HOH
HOH
436
A
HOH
437
4
HOH
HOH
437
A
HOH
438
4
HOH
HOH
438
A
HOH
439
4
HOH
HOH
439
A
HOH
440
4
HOH
HOH
440
A
HOH
441
4
HOH
HOH
441
A
HOH
442
4
HOH
HOH
442
A
HOH
443
4
HOH
HOH
443
A
HOH
444
4
HOH
HOH
444
A
HOH
445
4
HOH
HOH
445
A
HOH
446
4
HOH
HOH
446
A
HOH
447
4
HOH
HOH
447
A
HOH
448
4
HOH
HOH
448
A
HOH
449
4
HOH
HOH
449
A
HOH
450
4
HOH
HOH
450
A
HOH
451
4
HOH
HOH
451
A
HOH
452
4
HOH
HOH
452
A
HOH
453
4
HOH
HOH
453
A
HOH
454
4
HOH
HOH
454
A
HOH
455
4
HOH
HOH
455
A
HOH
456
4
HOH
HOH
456
A
HOH
457
4
HOH
HOH
457
A
HOH
458
4
HOH
HOH
458
A
HOH
459
4
HOH
HOH
459
A
HOH
460
4
HOH
HOH
460
A
HOH
461
4
HOH
HOH
461
A
n
1
-24
A
n
2
-23
A
n
3
-22
A
n
4
-21
A
n
5
-20
A
n
6
-19
A
n
7
-18
A
n
8
-17
A
n
9
-16
A
n
10
-15
A
n
11
-14
A
n
12
-13
A
n
13
-12
A
n
14
-11
A
n
15
-10
A
n
16
-9
A
n
17
-8
A
n
18
-7
A
n
19
-6
A
n
20
-5
A
n
21
-4
A
n
22
-3
A
n
23
-2
A
n
24
-1
A
n
25
0
A
MET
1
n
26
MET
1
A
GLY
2
n
27
GLY
2
A
SER
3
n
28
SER
3
A
ALA
4
n
29
ALA
4
A
PHE
5
n
30
PHE
5
A
VAL
6
n
31
VAL
6
A
PHE
7
n
32
PHE
7
A
LEU
8
n
33
LEU
8
A
GLU
9
n
34
GLU
9
A
ALA
10
n
35
ALA
10
A
SER
11
n
36
SER
11
A
LEU
12
n
37
LEU
12
A
GLU
13
n
38
GLU
13
A
LEU
14
n
39
LEU
14
A
ILE
15
n
40
ILE
15
A
PRO
16
n
41
PRO
16
A
GLN
17
n
42
GLN
17
A
LYS
18
n
43
LYS
18
A
ILE
19
n
44
ILE
19
A
ARG
20
n
45
ARG
20
A
GLY
21
n
46
GLY
21
A
HIS
22
n
47
HIS
22
A
PRO
23
n
48
PRO
23
A
ALA
24
n
49
ALA
24
A
VAL
25
n
50
VAL
25
A
ARG
26
n
51
ARG
26
A
ALA
27
n
52
ALA
27
A
ASP
28
n
53
ASP
28
A
ALA
29
n
54
ALA
29
A
ILE
30
n
55
ILE
30
A
ARG
31
n
56
ARG
31
A
ARG
32
n
57
ARG
32
A
GLY
33
n
58
GLY
33
A
LYS
34
n
59
LYS
34
A
ARG
35
n
60
ARG
35
A
PRO
36
n
61
PRO
36
A
GLU
37
n
62
GLU
37
A
LYS
38
n
63
LYS
38
A
ILE
39
n
64
ILE
39
A
LEU
40
n
65
LEU
40
A
LEU
41
n
66
LEU
41
A
ASP
42
n
67
ASP
42
A
ASP
43
n
68
ASP
43
A
SER
44
n
69
SER
44
A
LYS
45
n
70
LYS
45
A
HIS
46
n
71
HIS
46
A
HIS
47
n
72
HIS
47
A
THR
48
n
73
THR
48
A
ALA
49
n
74
ALA
49
A
MET
50
n
75
MET
50
A
LYS
51
n
76
LYS
51
A
SER
52
n
77
SER
52
A
LEU
53
n
78
LEU
53
A
GLU
54
n
79
GLU
54
A
PHE
55
n
80
PHE
55
A
ARG
56
n
81
ARG
56
A
GLU
57
n
82
GLU
57
A
LYS
58
n
83
LYS
58
A
ARG
59
n
84
ARG
59
A
GLY
60
n
85
GLY
60
A
ARG
61
n
86
ARG
61
A
PRO
62
n
87
PRO
62
A
ASP
63
n
88
ASP
63
A
ILE
64
n
89
ILE
64
A
VAL
65
n
90
VAL
65
A
HIS
66
n
91
HIS
66
A
GLN
67
n
92
GLN
67
A
CYS
68
n
93
CYS
68
A
LEU
69
n
94
LEU
69
A
LEU
70
n
95
LEU
70
A
LEU
71
n
96
LEU
71
A
LEU
72
n
97
LEU
72
A
LEU
73
n
98
LEU
73
A
ASP
74
n
99
ASP
74
A
SER
75
n
100
SER
75
A
PRO
76
n
101
PRO
76
A
LEU
77
n
102
LEU
77
A
ARG
78
n
103
ARG
78
A
ASP
79
n
104
ASP
79
A
PHE
80
n
105
PHE
80
A
GLU
81
n
106
GLU
81
A
VAL
82
n
107
VAL
82
A
TYR
83
n
108
TYR
83
A
VAL
84
n
109
VAL
84
A
HIS
85
n
110
HIS
85
A
THR
86
n
111
THR
86
A
LEU
87
n
112
LEU
87
A
ASN
88
n
113
ASN
88
A
GLY
89
n
114
GLY
89
A
GLU
90
n
115
GLU
90
A
ILE
91
n
116
ILE
91
A
ILE
92
n
117
ILE
92
A
TRP
93
n
118
TRP
93
A
VAL
94
n
119
VAL
94
A
ASN
95
n
120
ASN
95
A
ARG
96
n
121
ARG
96
A
GLU
97
n
122
GLU
97
A
THR
98
n
123
THR
98
A
ARG
99
n
124
ARG
99
A
LEU
100
n
125
LEU
100
A
PRO
101
n
126
PRO
101
A
ARG
102
n
127
ARG
102
A
ASN
103
n
128
ASN
103
A
TYR
104
n
129
TYR
104
A
ASN
105
n
130
ASN
105
A
ARG
106
n
131
ARG
106
A
PHE
107
n
132
PHE
107
A
VAL
108
n
133
VAL
108
A
GLY
109
n
134
GLY
109
A
LEU
110
n
135
LEU
110
A
MET
111
n
136
MET
111
A
GLU
112
n
137
GLU
112
A
LYS
113
n
138
LYS
113
A
LEU
114
n
139
LEU
114
A
PHE
115
n
140
PHE
115
A
GLU
116
n
141
GLU
116
A
GLU
117
n
142
GLU
117
A
ARG
118
n
143
ARG
118
A
ARG
119
n
144
ARG
119
A
ILE
120
n
145
ILE
120
A
THR
121
n
146
THR
121
A
ALA
122
n
147
ALA
122
A
GLY
123
n
148
GLY
123
A
ASP
124
n
149
ASP
124
A
THR
125
n
150
THR
125
A
THR
126
n
151
THR
126
A
LEU
127
n
152
LEU
127
A
ILE
128
n
153
ILE
128
A
GLU
129
n
154
GLU
129
A
PHE
130
n
155
PHE
130
A
LYS
131
n
156
LYS
131
A
ASP
132
n
157
ASP
132
A
VAL
133
n
158
VAL
133
A
GLY
134
n
159
GLY
134
A
LEU
135
n
160
LEU
135
A
ARG
136
n
161
ARG
136
A
ASP
137
n
162
ASP
137
A
ILE
138
n
163
ILE
138
A
VAL
139
n
164
VAL
139
A
ARG
140
n
165
ARG
140
A
GLY
141
n
166
GLY
141
A
ARG
142
n
167
ARG
142
A
ASP
143
n
168
ASP
143
A
VAL
144
n
169
VAL
144
A
LEU
145
n
170
LEU
145
A
LEU
146
n
171
LEU
146
A
PHE
147
n
172
PHE
147
A
ARG
148
n
173
ARG
148
A
GLU
149
n
174
GLU
149
A
LYS
150
n
175
LYS
150
A
GLY
151
n
176
GLY
151
A
GLY
152
n
177
GLY
152
A
ARG
153
n
178
ARG
153
A
PHE
154
n
179
PHE
154
A
GLU
155
n
180
GLU
155
A
PHE
156
n
181
PHE
156
A
SER
157
n
182
SER
157
A
GLU
158
n
183
GLU
158
A
LEU
159
n
184
LEU
159
A
LEU
160
n
185
LEU
160
A
ASP
161
n
186
ASP
161
A
GLY
162
n
187
GLY
162
A
ASP
163
n
188
ASP
163
A
VAL
164
n
189
VAL
164
A
ALA
165
n
190
ALA
165
A
VAL
166
n
191
VAL
166
A
CYS
167
n
192
CYS
167
A
ILE
168
n
193
ILE
168
A
GLY
169
n
194
GLY
169
A
ALA
170
n
195
ALA
170
A
PHE
171
n
196
PHE
171
A
PRO
172
n
197
PRO
172
A
HIS
173
n
198
HIS
173
A
GLY
174
n
199
GLY
174
A
ASP
175
n
200
ASP
175
A
PHE
176
n
201
PHE
176
A
PHE
177
n
202
PHE
177
A
GLU
178
n
203
GLU
178
A
GLU
179
n
204
GLU
179
A
THR
180
n
205
THR
180
A
LEU
181
n
206
LEU
181
A
ARG
182
n
207
ARG
182
A
GLU
183
n
208
GLU
183
A
LEU
184
n
209
LEU
184
A
GLY
185
n
210
GLY
185
A
GLU
186
n
211
GLU
186
A
PHE
187
n
212
PHE
187
A
LYS
188
n
213
LYS
188
A
GLU
189
n
214
GLU
189
A
VAL
190
n
215
VAL
190
A
SER
191
n
216
SER
191
A
LEU
192
n
217
LEU
192
A
GLY
193
n
218
GLY
193
A
THR
194
n
219
THR
194
A
GLU
195
n
220
GLU
195
A
SER
196
n
221
SER
196
A
TYR
197
n
222
TYR
197
A
THR
198
n
223
THR
198
A
SER
199
n
224
SER
199
A
LEU
200
n
225
LEU
200
A
TYR
201
n
226
TYR
201
A
VAL
202
n
227
VAL
202
A
THR
203
n
228
THR
203
A
SER
204
n
229
SER
204
A
ARG
205
n
230
ARG
205
A
VAL
206
n
231
VAL
206
A
LEU
207
n
232
LEU
207
A
CYS
208
n
233
CYS
208
A
GLU
209
n
234
GLU
209
A
TYR
210
n
235
TYR
210
A
GLU
211
n
236
GLU
211
A
ARG
212
n
237
ARG
212
A
VAL
213
n
238
VAL
213
A
ARG
214
n
239
ARG
214
A
ALA
215
n
240
ALA
215
A
HIS
216
n
241
HIS
216
A
n
242
217
A
n
243
218
A
n
244
219
A
author_and_software_defined_assembly
PISA
2
dimeric
2420
-9
18830
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
-0.5000000000
-0.8660254038
0.0000000000
-0.8660254038
0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
6_555
-x,-x+y,-z+1/3
crystal symmetry operation
0.0000000000
0.0000000000
31.7300000000
A
N
ALA
122
A
N
ALA
147
A
O
THR
125
A
O
THR
150
A
O
GLU
129
A
O
GLU
154
A
N
TRP
93
A
N
TRP
118
A
O
ILE
92
A
O
ILE
117
A
N
VAL
84
A
N
VAL
109
A
O
HIS
85
A
O
HIS
110
A
N
PHE
7
A
N
PHE
32
A
N
VAL
6
A
N
VAL
31
A
O
VAL
166
A
O
VAL
191
A
O
ALA
165
A
O
ALA
190
A
N
LEU
145
A
N
LEU
170
A
N
LEU
146
A
N
LEU
171
A
O
VAL
190
A
O
VAL
215
1
A
CG
ARG
31
A
CG
ARG
56
1
Y
1
A
CD
ARG
31
A
CD
ARG
56
1
Y
1
A
NE
ARG
31
A
NE
ARG
56
1
Y
1
A
CZ
ARG
31
A
CZ
ARG
56
1
Y
1
A
NH1
ARG
31
A
NH1
ARG
56
1
Y
1
A
NH2
ARG
31
A
NH2
ARG
56
1
Y
1
A
CG
HIS
216
A
CG
HIS
241
1
Y
1
A
ND1
HIS
216
A
ND1
HIS
241
1
Y
1
A
CD2
HIS
216
A
CD2
HIS
241
1
Y
1
A
CE1
HIS
216
A
CE1
HIS
241
1
Y
1
A
NE2
HIS
216
A
NE2
HIS
241
1
Y
1
A
OXT
SAH
301
C
OXT
SAH
1
1
N
1
A
HIS
-24
A
HIS
1
1
Y
1
A
HIS
-23
A
HIS
2
1
Y
1
A
HIS
-22
A
HIS
3
1
Y
1
A
HIS
-21
A
HIS
4
1
Y
1
A
HIS
-20
A
HIS
5
1
Y
1
A
HIS
-19
A
HIS
6
1
Y
1
A
ARG
-18
A
ARG
7
1
Y
1
A
SER
-17
A
SER
8
1
Y
1
A
ASP
-16
A
ASP
9
1
Y
1
A
ILE
-15
A
ILE
10
1
Y
1
A
THR
-14
A
THR
11
1
Y
1
A
SER
-13
A
SER
12
1
Y
1
A
LEU
-12
A
LEU
13
1
Y
1
A
TYR
-11
A
TYR
14
1
Y
1
A
LYS
-10
A
LYS
15
1
Y
1
A
LYS
-9
A
LYS
16
1
Y
1
A
VAL
-8
A
VAL
17
1
Y
1
A
GLY
-7
A
GLY
18
1
Y
1
A
GLU
-6
A
GLU
19
1
Y
1
A
ASN
-5
A
ASN
20
1
Y
1
A
LEU
-4
A
LEU
21
1
Y
1
A
TYR
-3
A
TYR
22
1
Y
1
A
PHE
-2
A
PHE
23
1
Y
1
A
GLN
-1
A
GLN
24
1
Y
1
A
GLY
0
A
GLY
25
1
Y
1
A
LYS
217
A
LYS
242
1
Y
1
A
VAL
218
A
VAL
243
1
Y
1
A
GLY
219
A
GLY
244
1
Y
1
A
A
O
O
HOH
HOH
318
320
2.15
1
A
PHE
55
38.26
44.89
1
A
ARG
118
76.75
-11.57
1
A
ARG
118
76.75
-9.97
1
A
LEU
160
-98.99
47.05
1
A
ASP
161
-77.99
-99.81
23.45
0.00000
0.00000
0.00000
0.00000
0.00000
0.00000
0.9630
0.9580
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.211
0.198
0.199
1.45
28.90
2437
48192
48192
5.100
99.8
1.000
0.000
1.150
0.045
RANDOM
1
THROUGHOUT
0.000
SAD
0.066
0.8000
0.8000
1.2000
MAXIMUM LIKELIHOOD
MASK
1.45
28.90
240
2031
38
0
1753
0.2880
0.2650
1.4900
173
3315
3488
20
98.8100
1.450
28.900
3O7B
48192
0.000
0.07500
1
32.9000
14.300
99.8
1.45
1.50
5.800
0.51700
10.00
100.0
data reduction
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
DENZO
package
data scaling
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
SCALEPACK
package
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
5.2.0019
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
SHARP
Ribosome biogenesis Nep1 RNA methyltransferase
Crystal structure of Archaeoglobus Fulgidus Nep1 bound to S-adenosylhomocysteine
1
N
N
2
N
N
3
N
N
4
N
N
AfNep1 is a biological dimer by symmetry operation x,y,z.
A
PRO
16
A
PRO
41
HELX_P
A
ARG
20
A
ARG
45
5
1
5
A
HIS
22
A
HIS
47
HELX_P
A
GLY
33
A
GLY
58
1
2
12
A
ARG
35
A
ARG
60
HELX_P
A
ILE
39
A
ILE
64
5
3
5
A
ASP
42
A
ASP
67
HELX_P
A
HIS
47
A
HIS
72
1
4
6
A
THR
48
A
THR
73
HELX_P
A
MET
50
A
MET
75
5
5
3
A
PHE
55
A
PHE
80
HELX_P
A
ARG
59
A
ARG
84
5
6
5
A
PRO
62
A
PRO
87
HELX_P
A
ASP
74
A
ASP
99
1
7
13
A
ASN
103
A
ASN
128
HELX_P
A
ARG
118
A
ARG
143
1
8
16
A
GLY
134
A
GLY
159
HELX_P
A
VAL
139
A
VAL
164
1
9
6
A
GLU
155
A
GLU
180
HELX_P
A
LEU
160
A
LEU
185
1
10
6
A
PHE
177
A
PHE
202
HELX_P
A
GLY
185
A
GLY
210
1
11
9
A
THR
198
A
THR
223
HELX_P
A
ALA
215
A
ALA
240
1
12
18
disulf
2.643
A
CYS
208
A
SG
CYS
233
1_555
A
CYS
208
A
SG
CYS
233
6_555
TRANSFERASE
SPOUT, ribosome biogenesis, methyltransferase, rRNA processing, TRANSFERASE
A
ALA
215
A
ALA
240
1
A
HIS
216
A
HIS
241
0.14
NEP1_ARCFU
UNP
1
1
O29524
MGSAFVFLEASLELIPQKIRGHPAVRADAIRRGKRPEKILLDDSKHHTAMKSLEFREKRGRPDIVHQCLLLLLDSPLRDF
EVYVHTLNGEIIWVNRETRLPRNYNRFVGLMEKLFEERRITAGDTTLIEFKDVGLRDIVRGRDVLLFREKGGRFEFSELL
DGDVAVCIGAFPHGDFFEETLRELGEFKEVSLGTESYTSLYVTSRVLCEYERVRAHKVG
1
219
3O7B
1
219
O29524
A
1
26
244
1
EXPRESSION TAG
HIS
-24
3O7B
A
O29524
UNP
1
1
EXPRESSION TAG
HIS
-23
3O7B
A
O29524
UNP
2
1
EXPRESSION TAG
HIS
-22
3O7B
A
O29524
UNP
3
1
EXPRESSION TAG
HIS
-21
3O7B
A
O29524
UNP
4
1
EXPRESSION TAG
HIS
-20
3O7B
A
O29524
UNP
5
1
EXPRESSION TAG
HIS
-19
3O7B
A
O29524
UNP
6
1
EXPRESSION TAG
ARG
-18
3O7B
A
O29524
UNP
7
1
EXPRESSION TAG
SER
-17
3O7B
A
O29524
UNP
8
1
EXPRESSION TAG
ASP
-16
3O7B
A
O29524
UNP
9
1
EXPRESSION TAG
ILE
-15
3O7B
A
O29524
UNP
10
1
EXPRESSION TAG
THR
-14
3O7B
A
O29524
UNP
11
1
EXPRESSION TAG
SER
-13
3O7B
A
O29524
UNP
12
1
EXPRESSION TAG
LEU
-12
3O7B
A
O29524
UNP
13
1
EXPRESSION TAG
TYR
-11
3O7B
A
O29524
UNP
14
1
EXPRESSION TAG
LYS
-10
3O7B
A
O29524
UNP
15
1
EXPRESSION TAG
LYS
-9
3O7B
A
O29524
UNP
16
1
EXPRESSION TAG
VAL
-8
3O7B
A
O29524
UNP
17
1
EXPRESSION TAG
GLY
-7
3O7B
A
O29524
UNP
18
1
EXPRESSION TAG
GLU
-6
3O7B
A
O29524
UNP
19
1
EXPRESSION TAG
ASN
-5
3O7B
A
O29524
UNP
20
1
EXPRESSION TAG
LEU
-4
3O7B
A
O29524
UNP
21
1
EXPRESSION TAG
TYR
-3
3O7B
A
O29524
UNP
22
1
EXPRESSION TAG
PHE
-2
3O7B
A
O29524
UNP
23
1
EXPRESSION TAG
GLN
-1
3O7B
A
O29524
UNP
24
1
EXPRESSION TAG
GLY
0
3O7B
A
O29524
UNP
25
8
anti-parallel
anti-parallel
anti-parallel
parallel
parallel
parallel
parallel
A
ARG
119
A
ARG
144
A
ALA
122
A
ALA
147
A
THR
125
A
THR
150
A
LYS
131
A
LYS
156
A
ILE
91
A
ILE
116
A
VAL
94
A
VAL
119
A
PHE
80
A
PHE
105
A
THR
86
A
THR
111
A
SER
3
A
SER
28
A
ALA
10
A
ALA
35
A
VAL
164
A
VAL
189
A
GLY
169
A
GLY
194
A
ASP
143
A
ASP
168
A
PHE
147
A
PHE
172
A
PHE
187
A
PHE
212
A
VAL
190
A
VAL
215
BINDING SITE FOR RESIDUE TYR A 220
Software
5
BINDING SITE FOR RESIDUE SAH A 301
Software
20
A
ARG
153
A
ARG
178
5
1_555
A
SER
191
A
SER
216
5
1_555
A
LEU
192
A
LEU
217
5
1_555
A
GLY
193
A
GLY
218
5
1_555
A
ARG
205
A
ARG
230
5
1_555
A
PHE
147
A
PHE
172
20
1_555
A
ARG
148
A
ARG
173
20
1_555
A
GLU
149
A
GLU
174
20
1_555
A
ILE
168
A
ILE
193
20
1_555
A
GLY
169
A
GLY
194
20
1_555
A
PHE
171
A
PHE
196
20
1_555
A
GLY
174
A
GLY
199
20
1_555
A
PHE
176
A
PHE
201
20
1_555
A
VAL
190
A
VAL
215
20
1_555
A
SER
191
A
SER
216
20
1_555
A
LEU
192
A
LEU
217
20
1_555
A
GLY
193
A
GLY
218
20
1_555
A
GLU
195
A
GLU
220
20
1_555
A
SER
196
A
SER
221
20
1_555
A
TYR
197
A
TYR
222
20
1_555
A
SER
199
A
SER
224
20
1_555
A
VAL
202
A
VAL
227
20
1_555
A
HOH
238
D
HOH
20
1_555
A
HOH
320
D
HOH
20
1_555
A
HOH
383
D
HOH
20
1_555
152
P 31 2 1