0.012137
0.000000
0.000000
0.000000
0.012137
0.000000
0.000000
0.000000
0.013351
0.00000
0.00000
0.00000
Czudnochowski, N.
Finer-Moore, J.S.
Stroud, R.M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
82.390
82.390
74.900
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
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
Pt 2
195.078
PLATINUM (II) ION
non-polymer
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
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
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
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
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
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
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
CL
N
75
N
N
N
76
R
C
N
77
N
C
N
78
N
O
N
79
N
C
N
80
N
S
N
81
N
O
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
N
N
90
S
C
N
91
N
C
N
92
N
O
N
93
N
C
N
94
N
C
N
95
N
C
N
96
N
O
N
97
N
N
N
98
N
O
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
N
N
110
S
C
N
111
N
C
N
112
N
O
N
113
N
C
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
O
N
118
N
O
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
N
N
129
N
C
N
130
N
C
N
131
N
O
N
132
N
O
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
N
N
139
S
C
N
140
N
C
N
141
N
O
N
142
N
C
Y
143
N
C
Y
144
N
N
Y
145
N
C
Y
146
N
C
Y
147
N
N
N
148
N
O
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
O
N
160
N
H
N
161
N
H
N
162
N
N
N
163
S
C
N
164
N
C
N
165
N
O
N
166
S
C
N
167
N
C
N
168
N
C
N
169
N
C
N
170
N
O
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
N
N
185
S
C
N
186
N
C
N
187
N
O
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
C
N
192
N
O
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
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
N
N
207
S
C
N
208
N
C
N
209
N
O
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
C
N
214
N
N
N
215
N
O
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
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
N
N
232
S
C
N
233
N
C
N
234
N
O
N
235
N
C
N
236
N
C
N
237
N
S
N
238
N
C
N
239
N
O
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
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
N
N
252
S
C
N
253
N
C
N
254
N
O
N
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
Y
261
N
C
N
262
N
O
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
H
N
273
N
H
N
274
N
N
N
275
S
C
N
276
N
C
N
277
N
O
N
278
N
C
N
279
N
C
N
280
N
C
N
281
N
O
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
PT
N
292
N
N
N
293
S
C
N
294
N
C
N
295
N
O
N
296
N
C
N
297
N
O
N
298
N
O
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
N
N
307
S
C
N
308
N
C
N
309
N
O
N
310
R
C
N
311
N
O
N
312
N
C
N
313
N
O
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
N
N
324
S
C
N
325
N
C
N
326
N
O
N
327
N
C
Y
328
N
C
Y
329
N
C
Y
330
N
C
Y
331
N
N
Y
332
N
C
Y
333
N
C
Y
334
N
C
Y
335
N
C
Y
336
N
C
N
337
N
O
N
338
N
H
N
339
N
H
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
H
N
348
N
H
N
349
N
H
N
350
N
N
N
351
S
C
N
352
N
C
N
353
N
O
N
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
Y
359
N
C
Y
360
N
C
N
361
N
O
N
362
N
O
N
363
N
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
N
N
375
S
C
N
376
N
C
N
377
N
O
N
378
N
C
N
379
N
C
N
380
N
C
N
381
N
O
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
H
N
392
N
H
N
1
N
sing
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
doub
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
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
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
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
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
doub
N
77
N
sing
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
sing
N
95
N
sing
N
96
N
sing
N
97
N
doub
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
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
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
sing
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
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
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
doub
N
159
N
sing
N
160
N
sing
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
sing
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
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
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
doub
N
201
N
sing
N
202
N
sing
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
sing
N
224
N
doub
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
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
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
doub
N
267
N
sing
N
268
N
sing
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
doub
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
doub
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
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
sing
N
311
N
sing
N
312
N
doub
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
Y
317
N
doub
Y
318
N
sing
Y
319
N
sing
N
320
N
sing
Y
321
N
doub
Y
322
N
sing
Y
323
N
sing
N
324
N
sing
Y
325
N
sing
Y
326
N
doub
N
327
N
sing
Y
328
N
doub
N
329
N
sing
Y
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
Y
345
N
doub
Y
346
N
sing
Y
347
N
sing
N
348
N
sing
Y
349
N
doub
N
350
N
sing
Y
351
N
doub
N
352
N
sing
Y
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
doub
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
UK
Nucleic Acids Res.
NARHAD
0389
0305-1048
42
2037
2048
10.1093/nar/gkt1050
24214967
The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs.
2014
10.2210/pdb4lab/pdb
pdb_00004lab
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
1
monochromator
CCD
2011-02-17
ADSC QUANTUM 315r
Si(111)
SINGLE WAVELENGTH
M
x-ray
1
1.068830
1.0
8.3.1
ALS
1.068830
SYNCHROTRON
ALS BEAMLINE 8.3.1
28552.619
Ribosomal large subunit pseudouridine synthase B
5.4.99.22
UNP Residues 1-251
1
man
polymer
195.078
PLATINUM (II) ION
2
syn
non-polymer
35.453
CHLORIDE ION
1
syn
non-polymer
18.015
water
19
nat
water
23S rRNA pseudouridine(2605) synthase, rRNA pseudouridylate synthase B, rRNA-uridine isomerase B
no
no
GPGSMSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRESAEQICRVLAYYKPE
GELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRDL
SRGVQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQ
TNYLRELVELPPETS
GPGSMSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRESAEQICRVLAYYKPE
GELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRDL
SRGVQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQ
TNYLRELVELPPETS
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
K12
sample
b1269, JW1261, rluB, yciL
83333
Escherichia coli
469008
Escherichia coli
BL21(DE3)
PLASMID
pET47 modified
1
2.23
44.74
VAPOR DIFFUSION, HANGING DROP
5.6
0.1M tri-Sodium citrate pH 5.6, 20% isopropanol, 15% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K
289
software
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Database references
Refinement description
Data collection
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
2013-11-20
1
1
2014-02-26
1
2
2017-11-15
1
3
2019-07-17
1
4
2023-09-20
_software.classification
_software.name
_software.version
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2013-06-19
REL
REL
PT
PLATINUM (II) ION
CL
CHLORIDE ION
HOH
water
2GML
PDB ENTRY 2GML
PDB
experimental model
PT
301
2
PT
PT
301
A
PT
302
2
PT
PT
302
A
CL
303
3
CL
CL
303
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
n
1
-3
A
n
2
-2
A
n
3
-1
A
n
4
0
A
n
5
1
A
n
6
2
A
n
7
3
A
n
8
4
A
n
9
5
A
n
10
6
A
n
11
7
A
n
12
8
A
n
13
9
A
n
14
10
A
n
15
11
A
n
16
12
A
n
17
13
A
n
18
14
A
n
19
15
A
n
20
16
A
n
21
17
A
n
22
18
A
n
23
19
A
n
24
20
A
n
25
21
A
n
26
22
A
n
27
23
A
n
28
24
A
n
29
25
A
n
30
26
A
n
31
27
A
n
32
28
A
n
33
29
A
n
34
30
A
n
35
31
A
n
36
32
A
n
37
33
A
n
38
34
A
n
39
35
A
n
40
36
A
n
41
37
A
n
42
38
A
n
43
39
A
n
44
40
A
n
45
41
A
n
46
42
A
n
47
43
A
n
48
44
A
n
49
45
A
n
50
46
A
n
51
47
A
n
52
48
A
n
53
49
A
n
54
50
A
n
55
51
A
n
56
52
A
n
57
53
A
n
58
54
A
n
59
55
A
n
60
56
A
n
61
57
A
n
62
58
A
n
63
59
A
n
64
60
A
n
65
61
A
n
66
62
A
n
67
63
A
n
68
64
A
GLN
65
n
69
GLN
65
A
ILE
66
n
70
ILE
66
A
CYS
67
n
71
CYS
67
A
ARG
68
n
72
ARG
68
A
VAL
69
n
73
VAL
69
A
LEU
70
n
74
LEU
70
A
ALA
71
n
75
ALA
71
A
TYR
72
n
76
TYR
72
A
TYR
73
n
77
TYR
73
A
LYS
74
n
78
LYS
74
A
PRO
75
n
79
PRO
75
A
GLU
76
n
80
GLU
76
A
GLY
77
n
81
GLY
77
A
GLU
78
n
82
GLU
78
A
LEU
79
n
83
LEU
79
A
CYS
80
n
84
CYS
80
A
THR
81
n
85
THR
81
A
ARG
82
n
86
ARG
82
A
ASN
83
n
87
ASN
83
A
ASP
84
n
88
ASP
84
A
PRO
85
n
89
PRO
85
A
GLU
86
n
90
GLU
86
A
GLY
87
n
91
GLY
87
A
ARG
88
n
92
ARG
88
A
PRO
89
n
93
PRO
89
A
THR
90
n
94
THR
90
A
VAL
91
n
95
VAL
91
A
PHE
92
n
96
PHE
92
A
ASP
93
n
97
ASP
93
A
ARG
94
n
98
ARG
94
A
LEU
95
n
99
LEU
95
A
PRO
96
n
100
PRO
96
A
LYS
97
n
101
LYS
97
A
LEU
98
n
102
LEU
98
A
ARG
99
n
103
ARG
99
A
GLY
100
n
104
GLY
100
A
ALA
101
n
105
ALA
101
A
ARG
102
n
106
ARG
102
A
TRP
103
n
107
TRP
103
A
ILE
104
n
108
ILE
104
A
ALA
105
n
109
ALA
105
A
VAL
106
n
110
VAL
106
A
GLY
107
n
111
GLY
107
A
ARG
108
n
112
ARG
108
A
LEU
109
n
113
LEU
109
A
ASP
110
n
114
ASP
110
A
VAL
111
n
115
VAL
111
A
ASN
112
n
116
ASN
112
A
THR
113
n
117
THR
113
A
CYS
114
n
118
CYS
114
A
GLY
115
n
119
GLY
115
A
LEU
116
n
120
LEU
116
A
LEU
117
n
121
LEU
117
A
LEU
118
n
122
LEU
118
A
PHE
119
n
123
PHE
119
A
THR
120
n
124
THR
120
A
THR
121
n
125
THR
121
A
ASP
122
n
126
ASP
122
A
GLY
123
n
127
GLY
123
A
GLU
124
n
128
GLU
124
A
LEU
125
n
129
LEU
125
A
ALA
126
n
130
ALA
126
A
ASN
127
n
131
ASN
127
A
ARG
128
n
132
ARG
128
A
LEU
129
n
133
LEU
129
A
MET
130
n
134
MET
130
A
HIS
131
n
135
HIS
131
A
PRO
132
n
136
PRO
132
A
SER
133
n
137
SER
133
A
ARG
134
n
138
ARG
134
A
GLU
135
n
139
GLU
135
A
VAL
136
n
140
VAL
136
A
GLU
137
n
141
GLU
137
A
ARG
138
n
142
ARG
138
A
GLU
139
n
143
GLU
139
A
TYR
140
n
144
TYR
140
A
ALA
141
n
145
ALA
141
A
VAL
142
n
146
VAL
142
A
ARG
143
n
147
ARG
143
A
VAL
144
n
148
VAL
144
A
PHE
145
n
149
PHE
145
A
GLY
146
n
150
GLY
146
A
GLN
147
n
151
GLN
147
A
VAL
148
n
152
VAL
148
A
ASP
149
n
153
ASP
149
A
ASP
150
n
154
ASP
150
A
ALA
151
n
155
ALA
151
A
LYS
152
n
156
LYS
152
A
LEU
153
n
157
LEU
153
A
ARG
154
n
158
ARG
154
A
ASP
155
n
159
ASP
155
A
LEU
156
n
160
LEU
156
A
SER
157
n
161
SER
157
A
ARG
158
n
162
ARG
158
A
GLY
159
n
163
GLY
159
A
VAL
160
n
164
VAL
160
A
GLN
161
n
165
GLN
161
A
LEU
162
n
166
LEU
162
A
GLU
163
n
167
GLU
163
A
ASP
164
n
168
ASP
164
A
GLY
165
n
169
GLY
165
A
PRO
166
n
170
PRO
166
A
ALA
167
n
171
ALA
167
A
ALA
168
n
172
ALA
168
A
PHE
169
n
173
PHE
169
A
LYS
170
n
174
LYS
170
A
THR
171
n
175
THR
171
A
ILE
172
n
176
ILE
172
A
LYS
173
n
177
LYS
173
A
PHE
174
n
178
PHE
174
A
SER
175
n
179
SER
175
A
GLY
176
n
180
GLY
176
A
GLY
177
n
181
GLY
177
A
GLU
178
n
182
GLU
178
A
GLY
179
n
183
GLY
179
A
ILE
180
n
184
ILE
180
A
ASN
181
n
185
ASN
181
A
GLN
182
n
186
GLN
182
A
TRP
183
n
187
TRP
183
A
TYR
184
n
188
TYR
184
A
ASN
185
n
189
ASN
185
A
VAL
186
n
190
VAL
186
A
THR
187
n
191
THR
187
A
LEU
188
n
192
LEU
188
A
THR
189
n
193
THR
189
A
GLU
190
n
194
GLU
190
A
GLY
191
n
195
GLY
191
A
ARG
192
n
196
ARG
192
A
ASN
193
n
197
ASN
193
A
ARG
194
n
198
ARG
194
A
GLU
195
n
199
GLU
195
A
VAL
196
n
200
VAL
196
A
ARG
197
n
201
ARG
197
A
ARG
198
n
202
ARG
198
A
LEU
199
n
203
LEU
199
A
TRP
200
n
204
TRP
200
A
GLU
201
n
205
GLU
201
A
ALA
202
n
206
ALA
202
A
VAL
203
n
207
VAL
203
A
GLY
204
n
208
GLY
204
A
VAL
205
n
209
VAL
205
A
GLN
206
n
210
GLN
206
A
VAL
207
n
211
VAL
207
A
SER
208
n
212
SER
208
A
ARG
209
n
213
ARG
209
A
LEU
210
n
214
LEU
210
A
ILE
211
n
215
ILE
211
A
ARG
212
n
216
ARG
212
A
VAL
213
n
217
VAL
213
A
ARG
214
n
218
ARG
214
A
TYR
215
n
219
TYR
215
A
GLY
216
n
220
GLY
216
A
ASP
217
n
221
ASP
217
A
ILE
218
n
222
ILE
218
A
PRO
219
n
223
PRO
219
A
LEU
220
n
224
LEU
220
A
PRO
221
n
225
PRO
221
A
LYS
222
n
226
LYS
222
A
GLY
223
n
227
GLY
223
A
LEU
224
n
228
LEU
224
A
PRO
225
n
229
PRO
225
A
ARG
226
n
230
ARG
226
A
GLY
227
n
231
GLY
227
A
GLY
228
n
232
GLY
228
A
TRP
229
n
233
TRP
229
A
THR
230
n
234
THR
230
A
GLU
231
n
235
GLU
231
A
LEU
232
n
236
LEU
232
A
ASP
233
n
237
ASP
233
A
LEU
234
n
238
LEU
234
A
ALA
235
n
239
ALA
235
A
GLN
236
n
240
GLN
236
A
THR
237
n
241
THR
237
A
ASN
238
n
242
ASN
238
A
TYR
239
n
243
TYR
239
A
LEU
240
n
244
LEU
240
A
ARG
241
n
245
ARG
241
A
GLU
242
n
246
GLU
242
A
LEU
243
n
247
LEU
243
A
VAL
244
n
248
VAL
244
A
GLU
245
n
249
GLU
245
A
LEU
246
n
250
LEU
246
A
PRO
247
n
251
PRO
247
A
PRO
248
n
252
PRO
248
A
GLU
249
n
253
GLU
249
A
THR
250
n
254
THR
250
A
SER
251
n
255
SER
251
A
3.9293
2.7754
-0.0873
8.1207
-0.4351
4.8960
-0.0755
0.4765
0.0950
-0.4616
0.0403
-0.3759
-0.0229
0.4250
0.0718
0.2672
0.0526
0.0007
0.4986
0.0423
0.2806
refined
40.8883
8.8979
24.9800
X-RAY DIFFRACTION
1.0967
0.5513
-0.7487
4.9251
-3.0206
4.4886
0.1668
0.1774
0.3592
0.4264
0.2178
0.6725
-0.6925
-0.6268
-0.3311
0.3787
0.0761
0.1062
0.5422
0.1086
0.5803
refined
34.3758
23.6706
27.2208
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
(chain A and resid 65:138)
X-RAY DIFFRACTION
2
(chain A and resid 139:251)
author_and_software_defined_assembly
PISA
1
monomeric
A
CYS
114
A
SG
CYS
118
1_555
A
PT
301
B
PT
PT
1_555
A
ARG
226
A
NH2
ARG
230
1_555
66.9
A
CYS
114
A
SG
CYS
118
1_555
A
PT
301
B
PT
PT
1_555
A
ARG
226
A
NE
ARG
230
1_555
98.2
A
ARG
226
A
NH2
ARG
230
1_555
A
PT
301
B
PT
PT
1_555
A
ARG
226
A
NE
ARG
230
1_555
52.4
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
ILE
104
A
N
ILE
108
A
O
THR
120
A
O
THR
124
A
N
CYS
114
A
N
CYS
118
A
O
LEU
210
A
O
LEU
214
A
N
TYR
215
A
N
TYR
219
A
O
ILE
218
A
O
ILE
222
A
N
LYS
173
A
N
LYS
177
A
O
ASN
185
A
O
ASN
189
A
O
TYR
184
A
O
TYR
188
A
N
VAL
142
A
N
VAL
146
A
N
ALA
141
A
N
ALA
145
A
O
ILE
211
A
O
ILE
215
A
O
LEU
210
A
O
LEU
214
A
N
CYS
114
A
N
CYS
118
A
O
GLY
115
A
O
GLY
119
A
N
LYS
74
A
N
LYS
78
A
N
ALA
71
A
N
ALA
75
A
O
THR
230
A
O
THR
234
A
N
VAL
160
A
N
VAL
164
A
O
ALA
167
A
O
ALA
171
1
A
CG
ARG
134
A
CG
ARG
138
1
Y
1
A
CD
ARG
134
A
CD
ARG
138
1
Y
1
A
NE
ARG
134
A
NE
ARG
138
1
Y
1
A
CZ
ARG
134
A
CZ
ARG
138
1
Y
1
A
NH1
ARG
134
A
NH1
ARG
138
1
Y
1
A
NH2
ARG
134
A
NH2
ARG
138
1
Y
1
A
CG
ARG
154
A
CG
ARG
158
1
Y
1
A
CD
ARG
154
A
CD
ARG
158
1
Y
1
A
NE
ARG
154
A
NE
ARG
158
1
Y
1
A
CZ
ARG
154
A
CZ
ARG
158
1
Y
1
A
NH1
ARG
154
A
NH1
ARG
158
1
Y
1
A
NH2
ARG
154
A
NH2
ARG
158
1
Y
1
A
CG
ARG
158
A
CG
ARG
162
1
Y
1
A
CD
ARG
158
A
CD
ARG
162
1
Y
1
A
NE
ARG
158
A
NE
ARG
162
1
Y
1
A
CZ
ARG
158
A
CZ
ARG
162
1
Y
1
A
NH1
ARG
158
A
NH1
ARG
162
1
Y
1
A
NH2
ARG
158
A
NH2
ARG
162
1
Y
1
A
CD
GLN
161
A
CD
GLN
165
1
Y
1
A
OE1
GLN
161
A
OE1
GLN
165
1
Y
1
A
NE2
GLN
161
A
NE2
GLN
165
1
Y
1
A
CG
LYS
170
A
CG
LYS
174
1
Y
1
A
CD
LYS
170
A
CD
LYS
174
1
Y
1
A
CE
LYS
170
A
CE
LYS
174
1
Y
1
A
NZ
LYS
170
A
NZ
LYS
174
1
Y
1
A
CG
ARG
194
A
CG
ARG
198
1
Y
1
A
CD
ARG
194
A
CD
ARG
198
1
Y
1
A
NE
ARG
194
A
NE
ARG
198
1
Y
1
A
CZ
ARG
194
A
CZ
ARG
198
1
Y
1
A
NH1
ARG
194
A
NH1
ARG
198
1
Y
1
A
NH2
ARG
194
A
NH2
ARG
198
1
Y
1
A
CD
ARG
209
A
CD
ARG
213
1
Y
1
A
NE
ARG
209
A
NE
ARG
213
1
Y
1
A
CZ
ARG
209
A
CZ
ARG
213
1
Y
1
A
NH1
ARG
209
A
NH1
ARG
213
1
Y
1
A
NH2
ARG
209
A
NH2
ARG
213
1
Y
1
A
CG
LYS
222
A
CG
LYS
226
1
Y
1
A
CD
LYS
222
A
CD
LYS
226
1
Y
1
A
CE
LYS
222
A
CE
LYS
226
1
Y
1
A
NZ
LYS
222
A
NZ
LYS
226
1
Y
1
A
GLY
-3
A
GLY
1
1
Y
1
A
PRO
-2
A
PRO
2
1
Y
1
A
GLY
-1
A
GLY
3
1
Y
1
A
SER
0
A
SER
4
1
Y
1
A
MET
1
A
MET
5
1
Y
1
A
SER
2
A
SER
6
1
Y
1
A
GLU
3
A
GLU
7
1
Y
1
A
LYS
4
A
LYS
8
1
Y
1
A
LEU
5
A
LEU
9
1
Y
1
A
GLN
6
A
GLN
10
1
Y
1
A
LYS
7
A
LYS
11
1
Y
1
A
VAL
8
A
VAL
12
1
Y
1
A
LEU
9
A
LEU
13
1
Y
1
A
ALA
10
A
ALA
14
1
Y
1
A
ARG
11
A
ARG
15
1
Y
1
A
ALA
12
A
ALA
16
1
Y
1
A
GLY
13
A
GLY
17
1
Y
1
A
HIS
14
A
HIS
18
1
Y
1
A
GLY
15
A
GLY
19
1
Y
1
A
SER
16
A
SER
20
1
Y
1
A
ARG
17
A
ARG
21
1
Y
1
A
ARG
18
A
ARG
22
1
Y
1
A
GLU
19
A
GLU
23
1
Y
1
A
ILE
20
A
ILE
24
1
Y
1
A
GLU
21
A
GLU
25
1
Y
1
A
SER
22
A
SER
26
1
Y
1
A
ILE
23
A
ILE
27
1
Y
1
A
ILE
24
A
ILE
28
1
Y
1
A
GLU
25
A
GLU
29
1
Y
1
A
ALA
26
A
ALA
30
1
Y
1
A
GLY
27
A
GLY
31
1
Y
1
A
ARG
28
A
ARG
32
1
Y
1
A
VAL
29
A
VAL
33
1
Y
1
A
SER
30
A
SER
34
1
Y
1
A
VAL
31
A
VAL
35
1
Y
1
A
ASP
32
A
ASP
36
1
Y
1
A
GLY
33
A
GLY
37
1
Y
1
A
LYS
34
A
LYS
38
1
Y
1
A
ILE
35
A
ILE
39
1
Y
1
A
ALA
36
A
ALA
40
1
Y
1
A
LYS
37
A
LYS
41
1
Y
1
A
LEU
38
A
LEU
42
1
Y
1
A
GLY
39
A
GLY
43
1
Y
1
A
ASP
40
A
ASP
44
1
Y
1
A
ARG
41
A
ARG
45
1
Y
1
A
VAL
42
A
VAL
46
1
Y
1
A
GLU
43
A
GLU
47
1
Y
1
A
VAL
44
A
VAL
48
1
Y
1
A
THR
45
A
THR
49
1
Y
1
A
PRO
46
A
PRO
50
1
Y
1
A
GLY
47
A
GLY
51
1
Y
1
A
LEU
48
A
LEU
52
1
Y
1
A
LYS
49
A
LYS
53
1
Y
1
A
ILE
50
A
ILE
54
1
Y
1
A
ARG
51
A
ARG
55
1
Y
1
A
ILE
52
A
ILE
56
1
Y
1
A
ASP
53
A
ASP
57
1
Y
1
A
GLY
54
A
GLY
58
1
Y
1
A
HIS
55
A
HIS
59
1
Y
1
A
LEU
56
A
LEU
60
1
Y
1
A
ILE
57
A
ILE
61
1
Y
1
A
SER
58
A
SER
62
1
Y
1
A
VAL
59
A
VAL
63
1
Y
1
A
ARG
60
A
ARG
64
1
Y
1
A
GLU
61
A
GLU
65
1
Y
1
A
SER
62
A
SER
66
1
Y
1
A
ALA
63
A
ALA
67
1
Y
1
A
GLU
64
A
GLU
68
1
Y
1
A
PRO
85
-67.54
2.90
1
A
SER
175
-86.25
-142.36
1
A
GLU
190
-88.68
-149.36
0.2605
0.2306
0.2322
2.5043
58.259
471
9317
9317
5.06
99.82
0.30
1
Isotropic with TLS parameters for 2 groups
2.00
MOLECULAR REPLACEMENT
31.41
1.20
1.30
PDB ENTRY 2GML
ML
FLAT BULK SOLVENT MODEL
2.5043
58.259
19
1481
3
0
1459
0.006
1494
0.917
2029
14.750
553
0.060
225
0.005
268
0.3198
0.2778
2.8666
148
2867
100.00
0.2974
0.2544
3.6116
147
2921
100.00
0.2362
0.2123
58.2743
176
3058
100.00
56.5
2.5
58.259
4LAB
9324
9324
-3.0
.099
1
21.52
18.9
99.4
1.53
2.5
2.6
2.6
1
17.5
94.2
refinement
PHENIX
(phenix.refine: 1.8_1069)
model building
PHENIX
refinement
ELVES
data reduction
XDS
data scaling
XDS
phasing
PHENIX
Crystal structure of the catalytic domain of RluB
1
N
N
2
N
N
2
N
N
3
N
N
4
N
N
A
ASP
122
A
ASP
126
HELX_P
A
HIS
131
A
HIS
135
1
1
10
A
ASP
149
A
ASP
153
HELX_P
A
GLY
159
A
GLY
163
1
2
11
A
ARG
194
A
ARG
198
HELX_P
A
ALA
202
A
ALA
206
1
3
9
A
ASP
233
A
ASP
237
HELX_P
A
LEU
243
A
LEU
247
1
4
11
metalc
2.452
A
CYS
114
A
SG
CYS
118
1_555
A
PT
301
B
PT
PT
1_555
metalc
2.520
A
MET
130
A
SD
MET
134
1_555
A
PT
302
C
PT
PT
1_555
metalc
2.414
A
ARG
226
A
NH2
ARG
230
1_555
A
PT
301
B
PT
PT
1_555
metalc
2.764
A
ARG
226
A
NE
ARG
230
1_555
A
PT
301
B
PT
PT
1_555
RNA BINDING PROTEIN
beta sheet, alpha-beta protein, pseudouridine synthase, E. coli ribosomal RNA, RNA binding protein
RLUB_ECOLI
UNP
1
1
P37765
MSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRESAEQICRVLAYYKPEGELC
TRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGV
QLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYL
RELVELPPETSSKVAVEKDRRRMKANQIRRAVKRHSQVSGGRRSGGRNNNG
1
251
4LAB
1
251
P37765
A
1
5
255
1
expression tag
GLY
-3
4LAB
A
P37765
UNP
1
1
expression tag
PRO
-2
4LAB
A
P37765
UNP
2
1
expression tag
GLY
-1
4LAB
A
P37765
UNP
3
1
expression tag
SER
0
4LAB
A
P37765
UNP
4
4
7
2
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
A
ILE
104
A
ILE
108
A
ALA
105
A
ALA
109
A
CYS
114
A
CYS
118
A
THR
120
A
THR
124
A
VAL
207
A
VAL
211
A
TYR
215
A
TYR
219
A
ILE
218
A
ILE
222
A
PRO
219
A
PRO
223
A
THR
171
A
THR
175
A
GLU
178
A
GLU
182
A
ASN
181
A
ASN
185
A
LEU
188
A
LEU
192
A
ARG
138
A
ARG
142
A
VAL
144
A
VAL
148
A
VAL
207
A
VAL
211
A
TYR
215
A
TYR
219
A
CYS
114
A
CYS
118
A
THR
120
A
THR
124
A
VAL
69
A
VAL
73
A
LYS
74
A
LYS
78
A
TRP
229
A
TRP
233
A
GLU
231
A
GLU
235
A
VAL
160
A
VAL
164
A
LEU
162
A
LEU
166
A
GLY
165
A
GLY
169
A
ALA
167
A
ALA
171
BINDING SITE FOR RESIDUE PT A 301
A
PT
301
Software
4
BINDING SITE FOR RESIDUE PT A 302
A
PT
302
Software
3
BINDING SITE FOR RESIDUE CL A 303
A
CL
303
Software
2
A
CYS
114
A
CYS
118
4
1_555
A
ARG
209
A
ARG
213
4
1_555
A
ARG
226
A
ARG
230
4
1_555
A
CL
303
D
CL
4
1_555
A
GLY
107
A
GLY
111
3
1_555
A
MET
130
A
MET
134
3
1_555
A
TRP
229
A
TRP
233
3
3_544
A
ARG
209
A
ARG
213
2
1_555
A
PT
301
B
PT
2
1_555
96
P 43 21 2