0.01440
0.00000
0.00000
0.00000
0.01440
0.00000
0.00000
0.00000
0.00531
0.00000
0.00000
0.00000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.000
90.000
90.000
69.444
69.444
188.165
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
To be published
0353
Crystal structure of Peptide chain release factor 1 (RF-1) (SMU.1085) from Streptococcus mutans at 2.34 A resolution
10.2210/pdb1zbt/pdb
pdb_00001zbt
100
1
KOHZU: Double Crystal Si(111)
CCD
2005-01-21
ADSC QUANTUM 210
Double Crystal Si(111)
MAD
M
x-ray
1
0.99187
1.0
0.97960
1.0
0.97942
1.0
8.2.1
ALS
0.99187,0.97960,0.97942
SYNCHROTRON
ALS BEAMLINE 8.2.1
42635.152
Peptide chain release factor 1
1
man
polymer
18.015
water
61
nat
water
RF-1
no
yes
MGSDKIHHHHHH(MSE)NIYDQLQAVEDRYEELGELLSDPDVVSDTKRF(MSE)ELSREEANSRETVAVYREYKQVVQNI
ADAQE(MSE)IKDASGDPELEE(MSE)AKEELKNSKVAKEEYEEKLRFLLLPKDPNDDKNIILEIRGAAGGDEAALFAGD
LLN(MSE)YQKYAENQGWKFEV(MSE)EASANGVGGLKEVVA(MSE)VSGQSVYSKLKYESGAHRVQRVPVTESQGRVHT
STATVLV(MSE)PEVEEVEYEIDPKDLRVDIYHASGAGGQNVNKVATAVRIIHLPTNIKVE(MSE)QEERTQQKNRDKA
(MSE)KIIRARVADHFAQIAQDEQDAERKSTVGTGDRSERIRTYNFPQNRVTDHRIGLTLQKLDSILSGKLDEVIDALIL
YDQTQKLEELNK
MGSDKIHHHHHHMNIYDQLQAVEDRYEELGELLSDPDVVSDTKRFMELSREEANSRETVAVYREYKQVVQNIADAQEMIK
DASGDPELEEMAKEELKNSKVAKEEYEEKLRFLLLPKDPNDDKNIILEIRGAAGGDEAALFAGDLLNMYQKYAENQGWKF
EVMEASANGVGGLKEVVAMVSGQSVYSKLKYESGAHRVQRVPVTESQGRVHTSTATVLVMPEVEEVEYEIDPKDLRVDIY
HASGAGGQNVNKVATAVRIIHLPTNIKVEMQEERTQQKNRDKAMKIIRARVADHFAQIAQDEQDAERKSTVGTGDRSERI
RTYNFPQNRVTDHRIGLTLQKLDSILSGKLDEVIDALILYDQTQKLEELNK
A
358002
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Streptococcus
Escherichia
sample
prfA, rf1
1309
Streptococcus mutans
562
Escherichia coli
Plasmid
1
3.18
61.03
VAPOR DIFFUSION,SITTING DROP,NANODROP
6.5
13.0% PEG-8000, 0.2M Ca(OAc)2, 20.0% Glycerol, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
277
Joint Center for Structural Genomics
JCSG
PSI, Protein Structure Initiative
database_2
struct_conn
struct_ref_seq_dif
repository
Initial release
Version format compliance
Advisory
Version format compliance
Database references
Derived calculations
1
0
2005-05-03
1
1
2008-04-30
1
2
2011-07-13
1
3
2023-01-25
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
Y
RCSB
Y
RCSB
2005-04-08
REL
REL
HOH
water
HOH
1
2
HOH
HOH
360
A
HOH
2
2
HOH
HOH
361
A
HOH
3
2
HOH
HOH
362
A
HOH
4
2
HOH
HOH
363
A
HOH
5
2
HOH
HOH
364
A
HOH
6
2
HOH
HOH
365
A
HOH
7
2
HOH
HOH
366
A
HOH
8
2
HOH
HOH
367
A
HOH
9
2
HOH
HOH
368
A
HOH
10
2
HOH
HOH
369
A
HOH
11
2
HOH
HOH
370
A
HOH
12
2
HOH
HOH
371
A
HOH
13
2
HOH
HOH
372
A
HOH
14
2
HOH
HOH
373
A
HOH
15
2
HOH
HOH
374
A
HOH
16
2
HOH
HOH
375
A
HOH
17
2
HOH
HOH
376
A
HOH
18
2
HOH
HOH
377
A
HOH
19
2
HOH
HOH
378
A
HOH
20
2
HOH
HOH
379
A
HOH
21
2
HOH
HOH
380
A
HOH
22
2
HOH
HOH
381
A
HOH
23
2
HOH
HOH
382
A
HOH
24
2
HOH
HOH
383
A
HOH
25
2
HOH
HOH
384
A
HOH
26
2
HOH
HOH
385
A
HOH
27
2
HOH
HOH
386
A
HOH
28
2
HOH
HOH
387
A
HOH
29
2
HOH
HOH
388
A
HOH
30
2
HOH
HOH
389
A
HOH
31
2
HOH
HOH
390
A
HOH
32
2
HOH
HOH
391
A
HOH
33
2
HOH
HOH
392
A
HOH
34
2
HOH
HOH
393
A
HOH
35
2
HOH
HOH
394
A
HOH
36
2
HOH
HOH
395
A
HOH
37
2
HOH
HOH
396
A
HOH
38
2
HOH
HOH
397
A
HOH
39
2
HOH
HOH
398
A
HOH
40
2
HOH
HOH
399
A
HOH
41
2
HOH
HOH
400
A
HOH
42
2
HOH
HOH
401
A
HOH
43
2
HOH
HOH
402
A
HOH
44
2
HOH
HOH
403
A
HOH
45
2
HOH
HOH
404
A
HOH
46
2
HOH
HOH
405
A
HOH
47
2
HOH
HOH
406
A
HOH
48
2
HOH
HOH
407
A
HOH
49
2
HOH
HOH
408
A
HOH
50
2
HOH
HOH
409
A
HOH
51
2
HOH
HOH
410
A
HOH
52
2
HOH
HOH
411
A
HOH
53
2
HOH
HOH
412
A
HOH
54
2
HOH
HOH
413
A
HOH
55
2
HOH
HOH
414
A
HOH
56
2
HOH
HOH
415
A
HOH
57
2
HOH
HOH
416
A
HOH
58
2
HOH
HOH
417
A
HOH
59
2
HOH
HOH
418
A
HOH
60
2
HOH
HOH
419
A
HOH
61
2
HOH
HOH
420
A
n
1
-11
A
n
2
-10
A
n
3
-9
A
n
4
-8
A
n
5
-7
A
n
6
-6
A
n
7
-5
A
n
8
-4
A
n
9
-3
A
n
10
-2
A
HIS
-1
n
11
HIS
-1
A
HIS
0
n
12
HIS
0
A
MSE
1
n
13
MSE
1
A
ASN
2
n
14
ASN
2
A
ILE
3
n
15
ILE
3
A
TYR
4
n
16
TYR
4
A
ASP
5
n
17
ASP
5
A
GLN
6
n
18
GLN
6
A
LEU
7
n
19
LEU
7
A
GLN
8
n
20
GLN
8
A
ALA
9
n
21
ALA
9
A
VAL
10
n
22
VAL
10
A
GLU
11
n
23
GLU
11
A
ASP
12
n
24
ASP
12
A
ARG
13
n
25
ARG
13
A
TYR
14
n
26
TYR
14
A
GLU
15
n
27
GLU
15
A
GLU
16
n
28
GLU
16
A
LEU
17
n
29
LEU
17
A
n
30
18
A
n
31
19
A
n
32
20
A
n
33
21
A
n
34
22
A
n
35
23
A
n
36
24
A
n
37
25
A
n
38
26
A
n
39
27
A
n
40
28
A
n
41
29
A
n
42
30
A
n
43
31
A
n
44
32
A
n
45
33
A
n
46
34
A
n
47
35
A
n
48
36
A
n
49
37
A
ARG
38
n
50
ARG
38
A
GLU
39
n
51
GLU
39
A
GLU
40
n
52
GLU
40
A
ALA
41
n
53
ALA
41
A
ASN
42
n
54
ASN
42
A
SER
43
n
55
SER
43
A
ARG
44
n
56
ARG
44
A
GLU
45
n
57
GLU
45
A
THR
46
n
58
THR
46
A
VAL
47
n
59
VAL
47
A
ALA
48
n
60
ALA
48
A
VAL
49
n
61
VAL
49
A
TYR
50
n
62
TYR
50
A
ARG
51
n
63
ARG
51
A
GLU
52
n
64
GLU
52
A
TYR
53
n
65
TYR
53
A
LYS
54
n
66
LYS
54
A
GLN
55
n
67
GLN
55
A
VAL
56
n
68
VAL
56
A
VAL
57
n
69
VAL
57
A
GLN
58
n
70
GLN
58
A
ASN
59
n
71
ASN
59
A
ILE
60
n
72
ILE
60
A
ALA
61
n
73
ALA
61
A
ASP
62
n
74
ASP
62
A
ALA
63
n
75
ALA
63
A
GLN
64
n
76
GLN
64
A
GLU
65
n
77
GLU
65
A
MSE
66
n
78
MSE
66
A
n
79
67
A
n
80
68
A
n
81
69
A
n
82
70
A
n
83
71
A
n
84
72
A
n
85
73
A
PRO
74
n
86
PRO
74
A
GLU
75
n
87
GLU
75
A
LEU
76
n
88
LEU
76
A
GLU
77
n
89
GLU
77
A
GLU
78
n
90
GLU
78
A
MSE
79
n
91
MSE
79
A
ALA
80
n
92
ALA
80
A
LYS
81
n
93
LYS
81
A
GLU
82
n
94
GLU
82
A
GLU
83
n
95
GLU
83
A
LEU
84
n
96
LEU
84
A
LYS
85
n
97
LYS
85
A
ASN
86
n
98
ASN
86
A
SER
87
n
99
SER
87
A
LYS
88
n
100
LYS
88
A
VAL
89
n
101
VAL
89
A
ALA
90
n
102
ALA
90
A
LYS
91
n
103
LYS
91
A
GLU
92
n
104
GLU
92
A
GLU
93
n
105
GLU
93
A
TYR
94
n
106
TYR
94
A
GLU
95
n
107
GLU
95
A
GLU
96
n
108
GLU
96
A
LYS
97
n
109
LYS
97
A
LEU
98
n
110
LEU
98
A
ARG
99
n
111
ARG
99
A
PHE
100
n
112
PHE
100
A
LEU
101
n
113
LEU
101
A
LEU
102
n
114
LEU
102
A
LEU
103
n
115
LEU
103
A
PRO
104
n
116
PRO
104
A
LYS
105
n
117
LYS
105
A
ASP
106
n
118
ASP
106
A
PRO
107
n
119
PRO
107
A
ASN
108
n
120
ASN
108
A
ASP
109
n
121
ASP
109
A
ASP
110
n
122
ASP
110
A
LYS
111
n
123
LYS
111
A
ASN
112
n
124
ASN
112
A
ILE
113
n
125
ILE
113
A
ILE
114
n
126
ILE
114
A
LEU
115
n
127
LEU
115
A
GLU
116
n
128
GLU
116
A
ILE
117
n
129
ILE
117
A
ARG
118
n
130
ARG
118
A
GLY
119
n
131
GLY
119
A
ALA
120
n
132
ALA
120
A
ALA
121
n
133
ALA
121
A
GLY
122
n
134
GLY
122
A
GLY
123
n
135
GLY
123
A
ASP
124
n
136
ASP
124
A
GLU
125
n
137
GLU
125
A
ALA
126
n
138
ALA
126
A
ALA
127
n
139
ALA
127
A
LEU
128
n
140
LEU
128
A
PHE
129
n
141
PHE
129
A
ALA
130
n
142
ALA
130
A
GLY
131
n
143
GLY
131
A
ASP
132
n
144
ASP
132
A
LEU
133
n
145
LEU
133
A
LEU
134
n
146
LEU
134
A
ASN
135
n
147
ASN
135
A
MSE
136
n
148
MSE
136
A
TYR
137
n
149
TYR
137
A
GLN
138
n
150
GLN
138
A
LYS
139
n
151
LYS
139
A
TYR
140
n
152
TYR
140
A
ALA
141
n
153
ALA
141
A
GLU
142
n
154
GLU
142
A
ASN
143
n
155
ASN
143
A
GLN
144
n
156
GLN
144
A
GLY
145
n
157
GLY
145
A
TRP
146
n
158
TRP
146
A
LYS
147
n
159
LYS
147
A
PHE
148
n
160
PHE
148
A
GLU
149
n
161
GLU
149
A
VAL
150
n
162
VAL
150
A
MSE
151
n
163
MSE
151
A
GLU
152
n
164
GLU
152
A
ALA
153
n
165
ALA
153
A
SER
154
n
166
SER
154
A
ALA
155
n
167
ALA
155
A
ASN
156
n
168
ASN
156
A
GLY
157
n
169
GLY
157
A
VAL
158
n
170
VAL
158
A
GLY
159
n
171
GLY
159
A
GLY
160
n
172
GLY
160
A
LEU
161
n
173
LEU
161
A
LYS
162
n
174
LYS
162
A
GLU
163
n
175
GLU
163
A
VAL
164
n
176
VAL
164
A
VAL
165
n
177
VAL
165
A
ALA
166
n
178
ALA
166
A
MSE
167
n
179
MSE
167
A
VAL
168
n
180
VAL
168
A
SER
169
n
181
SER
169
A
GLY
170
n
182
GLY
170
A
GLN
171
n
183
GLN
171
A
SER
172
n
184
SER
172
A
VAL
173
n
185
VAL
173
A
TYR
174
n
186
TYR
174
A
SER
175
n
187
SER
175
A
LYS
176
n
188
LYS
176
A
LEU
177
n
189
LEU
177
A
LYS
178
n
190
LYS
178
A
TYR
179
n
191
TYR
179
A
GLU
180
n
192
GLU
180
A
SER
181
n
193
SER
181
A
GLY
182
n
194
GLY
182
A
ALA
183
n
195
ALA
183
A
HIS
184
n
196
HIS
184
A
ARG
185
n
197
ARG
185
A
VAL
186
n
198
VAL
186
A
GLN
187
n
199
GLN
187
A
ARG
188
n
200
ARG
188
A
VAL
189
n
201
VAL
189
A
PRO
190
n
202
PRO
190
A
VAL
191
n
203
VAL
191
A
THR
192
n
204
THR
192
A
GLU
193
n
205
GLU
193
A
SER
194
n
206
SER
194
A
GLN
195
n
207
GLN
195
A
GLY
196
n
208
GLY
196
A
ARG
197
n
209
ARG
197
A
VAL
198
n
210
VAL
198
A
HIS
199
n
211
HIS
199
A
THR
200
n
212
THR
200
A
SER
201
n
213
SER
201
A
THR
202
n
214
THR
202
A
ALA
203
n
215
ALA
203
A
THR
204
n
216
THR
204
A
VAL
205
n
217
VAL
205
A
LEU
206
n
218
LEU
206
A
VAL
207
n
219
VAL
207
A
MSE
208
n
220
MSE
208
A
PRO
209
n
221
PRO
209
A
GLU
210
n
222
GLU
210
A
VAL
211
n
223
VAL
211
A
GLU
212
n
224
GLU
212
A
GLU
213
n
225
GLU
213
A
VAL
214
n
226
VAL
214
A
GLU
215
n
227
GLU
215
A
TYR
216
n
228
TYR
216
A
GLU
217
n
229
GLU
217
A
ILE
218
n
230
ILE
218
A
ASP
219
n
231
ASP
219
A
PRO
220
n
232
PRO
220
A
LYS
221
n
233
LYS
221
A
ASP
222
n
234
ASP
222
A
LEU
223
n
235
LEU
223
A
ARG
224
n
236
ARG
224
A
VAL
225
n
237
VAL
225
A
ASP
226
n
238
ASP
226
A
ILE
227
n
239
ILE
227
A
TYR
228
n
240
TYR
228
A
HIS
229
n
241
HIS
229
A
ALA
230
n
242
ALA
230
A
n
243
231
A
n
244
232
A
n
245
233
A
n
246
234
A
n
247
235
A
n
248
236
A
n
249
237
A
n
250
238
A
n
251
239
A
LYS
240
n
252
LYS
240
A
VAL
241
n
253
VAL
241
A
ALA
242
n
254
ALA
242
A
THR
243
n
255
THR
243
A
ALA
244
n
256
ALA
244
A
VAL
245
n
257
VAL
245
A
ARG
246
n
258
ARG
246
A
ILE
247
n
259
ILE
247
A
ILE
248
n
260
ILE
248
A
HIS
249
n
261
HIS
249
A
LEU
250
n
262
LEU
250
A
PRO
251
n
263
PRO
251
A
THR
252
n
264
THR
252
A
ASN
253
n
265
ASN
253
A
ILE
254
n
266
ILE
254
A
LYS
255
n
267
LYS
255
A
VAL
256
n
268
VAL
256
A
GLU
257
n
269
GLU
257
A
MSE
258
n
270
MSE
258
A
GLN
259
n
271
GLN
259
A
GLU
260
n
272
GLU
260
A
GLU
261
n
273
GLU
261
A
ARG
262
n
274
ARG
262
A
THR
263
n
275
THR
263
A
GLN
264
n
276
GLN
264
A
GLN
265
n
277
GLN
265
A
LYS
266
n
278
LYS
266
A
ASN
267
n
279
ASN
267
A
ARG
268
n
280
ARG
268
A
ASP
269
n
281
ASP
269
A
LYS
270
n
282
LYS
270
A
ALA
271
n
283
ALA
271
A
MSE
272
n
284
MSE
272
A
LYS
273
n
285
LYS
273
A
ILE
274
n
286
ILE
274
A
ILE
275
n
287
ILE
275
A
ARG
276
n
288
ARG
276
A
ALA
277
n
289
ALA
277
A
ARG
278
n
290
ARG
278
A
VAL
279
n
291
VAL
279
A
ALA
280
n
292
ALA
280
A
ASP
281
n
293
ASP
281
A
HIS
282
n
294
HIS
282
A
PHE
283
n
295
PHE
283
A
ALA
284
n
296
ALA
284
A
GLN
285
n
297
GLN
285
A
ILE
286
n
298
ILE
286
A
ALA
287
n
299
ALA
287
A
GLN
288
n
300
GLN
288
A
ASP
289
n
301
ASP
289
A
GLU
290
n
302
GLU
290
A
GLN
291
n
303
GLN
291
A
ASP
292
n
304
ASP
292
A
ALA
293
n
305
ALA
293
A
n
306
294
A
n
307
295
A
n
308
296
A
n
309
297
A
THR
298
n
310
THR
298
A
VAL
299
n
311
VAL
299
A
GLY
300
n
312
GLY
300
A
THR
301
n
313
THR
301
A
GLY
302
n
314
GLY
302
A
ASP
303
n
315
ASP
303
A
ARG
304
n
316
ARG
304
A
SER
305
n
317
SER
305
A
GLU
306
n
318
GLU
306
A
ARG
307
n
319
ARG
307
A
ILE
308
n
320
ILE
308
A
ARG
309
n
321
ARG
309
A
THR
310
n
322
THR
310
A
TYR
311
n
323
TYR
311
A
ASN
312
n
324
ASN
312
A
PHE
313
n
325
PHE
313
A
PRO
314
n
326
PRO
314
A
GLN
315
n
327
GLN
315
A
ASN
316
n
328
ASN
316
A
ARG
317
n
329
ARG
317
A
VAL
318
n
330
VAL
318
A
THR
319
n
331
THR
319
A
ASP
320
n
332
ASP
320
A
HIS
321
n
333
HIS
321
A
ARG
322
n
334
ARG
322
A
ILE
323
n
335
ILE
323
A
GLY
324
n
336
GLY
324
A
LEU
325
n
337
LEU
325
A
THR
326
n
338
THR
326
A
LEU
327
n
339
LEU
327
A
GLN
328
n
340
GLN
328
A
LYS
329
n
341
LYS
329
A
LEU
330
n
342
LEU
330
A
ASP
331
n
343
ASP
331
A
SER
332
n
344
SER
332
A
ILE
333
n
345
ILE
333
A
LEU
334
n
346
LEU
334
A
SER
335
n
347
SER
335
A
GLY
336
n
348
GLY
336
A
LYS
337
n
349
LYS
337
A
LEU
338
n
350
LEU
338
A
ASP
339
n
351
ASP
339
A
GLU
340
n
352
GLU
340
A
VAL
341
n
353
VAL
341
A
ILE
342
n
354
ILE
342
A
ASP
343
n
355
ASP
343
A
ALA
344
n
356
ALA
344
A
LEU
345
n
357
LEU
345
A
ILE
346
n
358
ILE
346
A
LEU
347
n
359
LEU
347
A
TYR
348
n
360
TYR
348
A
ASP
349
n
361
ASP
349
A
GLN
350
n
362
GLN
350
A
THR
351
n
363
THR
351
A
GLN
352
n
364
GLN
352
A
LYS
353
n
365
LYS
353
A
LEU
354
n
366
LEU
354
A
GLU
355
n
367
GLU
355
A
GLU
356
n
368
GLU
356
A
LEU
357
n
369
LEU
357
A
ASN
358
n
370
ASN
358
A
n
371
359
A
3.6453
-3.0661
1.8500
4.9089
-4.5348
15.0597
0.1057
0.1355
-0.2483
-0.2464
-0.0724
0.0864
1.1578
0.2245
-0.0334
-0.0565
-0.0558
0.0866
0.3333
-0.1272
0.1853
refined
25.8679
40.0378
90.3676
X-RAY DIFFRACTION
2.2695
0.2705
2.3980
1.9056
0.2490
7.7041
0.1995
0.6711
-0.2114
-0.2614
0.0725
-0.1255
0.6626
0.5641
-0.2720
-0.1871
0.0236
0.0392
-0.2401
-0.0453
-0.1267
refined
58.0055
44.3855
74.9136
X-RAY DIFFRACTION
0.0516
0.1643
-0.1296
0.8362
1.1338
7.9665
-0.0038
0.1016
0.1187
-0.3090
0.0322
0.0805
-0.2882
-0.2367
-0.0283
-0.1891
-0.0452
0.0001
-0.1963
0.0038
-0.0186
refined
52.1119
48.4231
68.2666
X-RAY DIFFRACTION
A
74
A
86
A
104
A
116
X-RAY DIFFRACTION
1
ALL
A
105
A
117
A
210
A
222
X-RAY DIFFRACTION
2
ALL
A
298
A
310
A
358
A
370
X-RAY DIFFRACTION
3
ALL
author_defined_assembly
1
monomeric
A
MSE
1
SELENOMETHIONINE
A
MSE
13
MET
A
MSE
66
SELENOMETHIONINE
A
MSE
78
MET
A
MSE
79
SELENOMETHIONINE
A
MSE
91
MET
A
MSE
136
SELENOMETHIONINE
A
MSE
148
MET
A
MSE
151
SELENOMETHIONINE
A
MSE
163
MET
A
MSE
167
SELENOMETHIONINE
A
MSE
179
MET
A
MSE
208
SELENOMETHIONINE
A
MSE
220
MET
A
MSE
258
SELENOMETHIONINE
A
MSE
270
MET
A
MSE
272
SELENOMETHIONINE
A
MSE
284
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
SER
154
A
N
SER
166
A
O
GLU
163
A
O
GLU
175
A
O
ALA
166
A
O
ALA
178
A
N
LEU
115
A
N
LEU
127
A
N
ILE
114
A
N
ILE
126
A
O
MSE
208
A
O
MSE
220
A
O
SER
201
A
O
SER
213
A
N
VAL
186
A
N
VAL
198
A
N
ARG
185
A
N
ARG
197
A
O
ARG
309
A
O
ARG
321
A
N
THR
310
A
N
THR
322
A
O
THR
319
A
O
THR
331
A
N
VAL
318
A
N
VAL
330
A
O
LEU
327
A
O
LEU
339
A
N
ASP
226
A
N
ASP
238
A
O
ARG
246
A
O
ARG
258
A
N
HIS
249
A
N
HIS
261
A
O
ILE
254
A
O
ILE
266
1
A
CG
HIS
-1
A
CG
HIS
11
1
Y
1
A
ND1
HIS
-1
A
ND1
HIS
11
1
Y
1
A
CD2
HIS
-1
A
CD2
HIS
11
1
Y
1
A
CE1
HIS
-1
A
CE1
HIS
11
1
Y
1
A
NE2
HIS
-1
A
NE2
HIS
11
1
Y
1
A
CG
ARG
13
A
CG
ARG
25
1
Y
1
A
CD
ARG
13
A
CD
ARG
25
1
Y
1
A
NE
ARG
13
A
NE
ARG
25
1
Y
1
A
CZ
ARG
13
A
CZ
ARG
25
1
Y
1
A
NH1
ARG
13
A
NH1
ARG
25
1
Y
1
A
NH2
ARG
13
A
NH2
ARG
25
1
Y
1
A
CG
ARG
38
A
CG
ARG
50
1
Y
1
A
CD
ARG
38
A
CD
ARG
50
1
Y
1
A
NE
ARG
38
A
NE
ARG
50
1
Y
1
A
CZ
ARG
38
A
CZ
ARG
50
1
Y
1
A
NH1
ARG
38
A
NH1
ARG
50
1
Y
1
A
NH2
ARG
38
A
NH2
ARG
50
1
Y
1
A
CG
GLU
39
A
CG
GLU
51
1
Y
1
A
CD
GLU
39
A
CD
GLU
51
1
Y
1
A
OE1
GLU
39
A
OE1
GLU
51
1
Y
1
A
OE2
GLU
39
A
OE2
GLU
51
1
Y
1
A
CG
GLU
40
A
CG
GLU
52
1
Y
1
A
CD
GLU
40
A
CD
GLU
52
1
Y
1
A
OE1
GLU
40
A
OE1
GLU
52
1
Y
1
A
OE2
GLU
40
A
OE2
GLU
52
1
Y
1
A
CG
ARG
44
A
CG
ARG
56
1
Y
1
A
CD
ARG
44
A
CD
ARG
56
1
Y
1
A
NE
ARG
44
A
NE
ARG
56
1
Y
1
A
CZ
ARG
44
A
CZ
ARG
56
1
Y
1
A
NH1
ARG
44
A
NH1
ARG
56
1
Y
1
A
NH2
ARG
44
A
NH2
ARG
56
1
Y
1
A
CG
GLU
45
A
CG
GLU
57
1
Y
1
A
CD
GLU
45
A
CD
GLU
57
1
Y
1
A
OE1
GLU
45
A
OE1
GLU
57
1
Y
1
A
OE2
GLU
45
A
OE2
GLU
57
1
Y
1
A
CG
GLU
65
A
CG
GLU
77
1
Y
1
A
CD
GLU
65
A
CD
GLU
77
1
Y
1
A
OE1
GLU
65
A
OE1
GLU
77
1
Y
1
A
OE2
GLU
65
A
OE2
GLU
77
1
Y
1
A
CG
MSE
66
A
CG
MSE
78
1
Y
1
A
SE
MSE
66
A
SE
MSE
78
1
Y
1
A
CE
MSE
66
A
CE
MSE
78
1
Y
1
A
CG
GLU
75
A
CG
GLU
87
1
Y
1
A
CD
GLU
75
A
CD
GLU
87
1
Y
1
A
OE1
GLU
75
A
OE1
GLU
87
1
Y
1
A
OE2
GLU
75
A
OE2
GLU
87
1
Y
1
A
CG
GLU
77
A
CG
GLU
89
1
Y
1
A
CD
GLU
77
A
CD
GLU
89
1
Y
1
A
OE1
GLU
77
A
OE1
GLU
89
1
Y
1
A
OE2
GLU
77
A
OE2
GLU
89
1
Y
1
A
CG
LYS
81
A
CG
LYS
93
1
Y
1
A
CD
LYS
81
A
CD
LYS
93
1
Y
1
A
CE
LYS
81
A
CE
LYS
93
1
Y
1
A
NZ
LYS
81
A
NZ
LYS
93
1
Y
1
A
CG
LYS
85
A
CG
LYS
97
1
Y
1
A
CD
LYS
85
A
CD
LYS
97
1
Y
1
A
CE
LYS
85
A
CE
LYS
97
1
Y
1
A
NZ
LYS
85
A
NZ
LYS
97
1
Y
1
A
CG
GLU
92
A
CG
GLU
104
1
Y
1
A
CD
GLU
92
A
CD
GLU
104
1
Y
1
A
OE1
GLU
92
A
OE1
GLU
104
1
Y
1
A
OE2
GLU
92
A
OE2
GLU
104
1
Y
1
A
NE
ARG
99
A
NE
ARG
111
1
Y
1
A
CZ
ARG
99
A
CZ
ARG
111
1
Y
1
A
NH1
ARG
99
A
NH1
ARG
111
1
Y
1
A
NH2
ARG
99
A
NH2
ARG
111
1
Y
1
A
CD
GLU
142
A
CD
GLU
154
1
Y
1
A
OE1
GLU
142
A
OE1
GLU
154
1
Y
1
A
OE2
GLU
142
A
OE2
GLU
154
1
Y
1
A
CE
LYS
162
A
CE
LYS
174
1
Y
1
A
NZ
LYS
162
A
NZ
LYS
174
1
Y
1
A
CG
GLN
171
A
CG
GLN
183
1
Y
1
A
CD
GLN
171
A
CD
GLN
183
1
Y
1
A
OE1
GLN
171
A
OE1
GLN
183
1
Y
1
A
NE2
GLN
171
A
NE2
GLN
183
1
Y
1
A
CG
LYS
266
A
CG
LYS
278
1
Y
1
A
CD
LYS
266
A
CD
LYS
278
1
Y
1
A
CE
LYS
266
A
CE
LYS
278
1
Y
1
A
NZ
LYS
266
A
NZ
LYS
278
1
Y
1
A
OG1
THR
298
A
OG1
THR
310
1
Y
1
A
CG2
THR
298
A
CG2
THR
310
1
Y
1
A
CG
GLU
306
A
CG
GLU
318
1
Y
1
A
CD
GLU
306
A
CD
GLU
318
1
Y
1
A
OE1
GLU
306
A
OE1
GLU
318
1
Y
1
A
OE2
GLU
306
A
OE2
GLU
318
1
Y
1
A
MET
-11
A
MET
1
1
Y
1
A
GLY
-10
A
GLY
2
1
Y
1
A
SER
-9
A
SER
3
1
Y
1
A
ASP
-8
A
ASP
4
1
Y
1
A
LYS
-7
A
LYS
5
1
Y
1
A
ILE
-6
A
ILE
6
1
Y
1
A
HIS
-5
A
HIS
7
1
Y
1
A
HIS
-4
A
HIS
8
1
Y
1
A
HIS
-3
A
HIS
9
1
Y
1
A
HIS
-2
A
HIS
10
1
Y
1
A
GLY
18
A
GLY
30
1
Y
1
A
GLU
19
A
GLU
31
1
Y
1
A
LEU
20
A
LEU
32
1
Y
1
A
LEU
21
A
LEU
33
1
Y
1
A
SER
22
A
SER
34
1
Y
1
A
ASP
23
A
ASP
35
1
Y
1
A
PRO
24
A
PRO
36
1
Y
1
A
ASP
25
A
ASP
37
1
Y
1
A
VAL
26
A
VAL
38
1
Y
1
A
VAL
27
A
VAL
39
1
Y
1
A
SER
28
A
SER
40
1
Y
1
A
ASP
29
A
ASP
41
1
Y
1
A
THR
30
A
THR
42
1
Y
1
A
LYS
31
A
LYS
43
1
Y
1
A
ARG
32
A
ARG
44
1
Y
1
A
PHE
33
A
PHE
45
1
Y
1
A
MSE
34
A
MSE
46
1
Y
1
A
GLU
35
A
GLU
47
1
Y
1
A
LEU
36
A
LEU
48
1
Y
1
A
SER
37
A
SER
49
1
Y
1
A
ILE
67
A
ILE
79
1
Y
1
A
LYS
68
A
LYS
80
1
Y
1
A
ASP
69
A
ASP
81
1
Y
1
A
ALA
70
A
ALA
82
1
Y
1
A
SER
71
A
SER
83
1
Y
1
A
GLY
72
A
GLY
84
1
Y
1
A
ASP
73
A
ASP
85
1
Y
1
A
SER
231
A
SER
243
1
Y
1
A
GLY
232
A
GLY
244
1
Y
1
A
ALA
233
A
ALA
245
1
Y
1
A
GLY
234
A
GLY
246
1
Y
1
A
GLY
235
A
GLY
247
1
Y
1
A
GLN
236
A
GLN
248
1
Y
1
A
ASN
237
A
ASN
249
1
Y
1
A
VAL
238
A
VAL
250
1
Y
1
A
ASN
239
A
ASN
251
1
Y
1
A
GLU
294
A
GLU
306
1
Y
1
A
ARG
295
A
ARG
307
1
Y
1
A
LYS
296
A
LYS
308
1
Y
1
A
SER
297
A
SER
309
1
Y
1
A
LYS
359
A
LYS
371
1
Y
1
A
ARG
44
-29.62
-58.88
1
A
ALA
120
-103.48
-115.45
1
A
VAL
158
-152.92
37.88
1
A
SER
172
37.41
54.43
1
A
LYS
329
-142.11
21.17
1
A
LEU
357
-84.20
48.17
51.292
2.180
0.000
0.000
2.180
0.000
-4.360
0.940
0.903
OTHER REFINEMENT REMARKS:
1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
2). ELECTRON DENSITY FOR PORTIONS OF THE N-TERMINAL DOMAIN IS QUITE POOR;
THEREFORE, SEVERAL RESIDUES IN THIS REGION COULD NOT BE MODELED.
3). ELECTRON DENSITIES FOR TWO SURFACE LOOPS BETWEEN RESIDUES 231-239 AND
RESIDUES 294-297 ARE POOR. CONSEQUENTLY, THESE LOOPS WERE NOT MODELED.
0.275
0.221
0.223
0.22326
2.340
28.58
1033
19101
5.100
99.270
18.297
0.203
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
MAD
0.282
0.240
0.800
0.800
1.200
MAXIMUM LIKELIHOOD WITH PHASES
BABINET MODEL WITH MASK
2.340
28.58
61
2547
0
0
2486
0.013
0.022
2516
0.002
0.020
2287
1.255
1.960
3398
0.740
3.000
5301
6.109
5.000
315
33.180
25.360
125
16.843
15.000
447
20.346
15.000
16
0.068
0.200
390
0.003
0.020
2815
0.001
0.020
468
0.206
0.200
540
0.173
0.200
2405
0.175
0.200
1236
0.084
0.200
1633
0.114
0.200
79
0.172
0.200
7
0.162
0.200
46
0.114
0.200
9
1.650
3.000
1650
0.315
3.000
649
2.592
5.000
2536
4.814
8.000
988
6.639
11.000
862
0.363
0.3
2.401
70
1379
20
99.380
2.34
28.58
1ZBT
20155
0.088
1
8.100
3.500
99.600
2.34
2.47
1.300
2891
0.583
1
3.500
99.800
2.47
2.62
1.700
2722
0.463
1
3.600
100.000
2.62
2.80
2.400
2593
0.321
1
3.500
99.900
2.80
3.02
3.400
2424
0.227
1
3.500
100.000
3.02
3.31
5.500
2243
0.14
1
3.500
99.900
3.31
3.70
9.600
2019
0.079
1
3.500
99.700
3.70
4.27
13.800
1819
0.05
1
3.500
99.700
4.27
5.23
17.500
1532
0.039
1
3.500
99.200
5.23
7.40
15.700
1216
0.045
1
3.400
98.300
7.40
28.58
22.400
696
0.027
1
3.100
94.600
refinement
Murshudov, G.N.
ccp4@dl.ac.uk
Fortran
http://www.ccp4.ac.uk/main.html
REFMAC
program
5.2.0005
data scaling
Phil Evans
pre@mrc-lmb.cam.ac.uk
Fortran
http://www.ccp4.ac.uk/dist/html/INDEX.html
SCALA
program
data extraction
PDB
sw-help@rcsb.rutgers.edu
Jan. 30, 2005
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
1.600
data reduction
XDS
data scaling
CCP4
(SCALA)
phasing
SHARP
Crystal structure of Peptide chain release factor 1 (RF-1) (SMU.1085) from Streptococcus mutans at 2.34 A resolution
1
N
N
2
N
N
A
ASN
2
A
ASN
14
HELX_P
A
LEU
17
A
LEU
29
1
1
16
A
GLU
39
A
GLU
51
HELX_P
A
MSE
66
A
MSE
78
1
2
28
A
PRO
74
A
PRO
86
HELX_P
A
PHE
100
A
PHE
112
1
3
27
A
GLY
123
A
GLY
135
HELX_P
A
GLY
145
A
GLY
157
1
4
23
A
SER
172
A
SER
184
HELX_P
A
LYS
178
A
LYS
190
1
5
7
A
TYR
179
A
TYR
191
HELX_P
A
SER
181
A
SER
193
5
6
3
A
GLU
212
A
GLU
224
HELX_P
A
TYR
216
A
TYR
228
5
7
5
A
ASP
219
A
ASP
231
HELX_P
A
LYS
221
A
LYS
233
5
8
3
A
THR
263
A
THR
275
HELX_P
A
GLN
291
A
GLN
303
1
9
29
A
LYS
329
A
LYS
341
HELX_P
A
SER
335
A
SER
347
1
10
7
A
LEU
338
A
LEU
350
HELX_P
A
LEU
357
A
LEU
369
1
11
20
covale
1.329
both
A
HIS
0
A
C
HIS
12
1_555
A
MSE
1
A
N
MSE
13
1_555
covale
1.327
both
A
MSE
1
A
C
MSE
13
1_555
A
ASN
2
A
N
ASN
14
1_555
covale
1.337
both
A
GLU
65
A
C
GLU
77
1_555
A
MSE
66
A
N
MSE
78
1_555
covale
1.332
both
A
GLU
78
A
C
GLU
90
1_555
A
MSE
79
A
N
MSE
91
1_555
covale
1.331
both
A
MSE
79
A
C
MSE
91
1_555
A
ALA
80
A
N
ALA
92
1_555
covale
1.328
both
A
ASN
135
A
C
ASN
147
1_555
A
MSE
136
A
N
MSE
148
1_555
covale
1.323
both
A
MSE
136
A
C
MSE
148
1_555
A
TYR
137
A
N
TYR
149
1_555
covale
1.324
both
A
VAL
150
A
C
VAL
162
1_555
A
MSE
151
A
N
MSE
163
1_555
covale
1.322
both
A
MSE
151
A
C
MSE
163
1_555
A
GLU
152
A
N
GLU
164
1_555
covale
1.320
both
A
ALA
166
A
C
ALA
178
1_555
A
MSE
167
A
N
MSE
179
1_555
covale
1.336
both
A
MSE
167
A
C
MSE
179
1_555
A
VAL
168
A
N
VAL
180
1_555
covale
1.325
both
A
VAL
207
A
C
VAL
219
1_555
A
MSE
208
A
N
MSE
220
1_555
covale
1.345
both
A
MSE
208
A
C
MSE
220
1_555
A
PRO
209
A
N
PRO
221
1_555
covale
1.323
both
A
GLU
257
A
C
GLU
269
1_555
A
MSE
258
A
N
MSE
270
1_555
covale
1.327
both
A
MSE
258
A
C
MSE
270
1_555
A
GLN
259
A
N
GLN
271
1_555
covale
1.324
both
A
ALA
271
A
C
ALA
283
1_555
A
MSE
272
A
N
MSE
284
1_555
covale
1.339
both
A
MSE
272
A
C
MSE
284
1_555
A
LYS
273
A
N
LYS
285
1_555
TRANSLATION
SMU.1085, Peptide chain release factor 1 (RF-1), Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, TRANSLATION
RF1_STRMU
UNP
1
1
Q8DU64
MNIYDQLQAVEDRYEELGELLSDPDVVSDTKRFMELSREEANSRETVAVYREYKQVVQNIADAQEMIKDASGDPELEEMA
KEELKNSKVAKEEYEEKLRFLLLPKDPNDDKNIILEIRGAAGGDEAALFAGDLLNMYQKYAENQGWKFEVMEASANGVGG
LKEVVAMVSGQSVYSKLKYESGAHRVQRVPVTESQGRVHTSTATVLVMPEVEEVEYEIDPKDLRVDIYHASGAGGQNVNK
VATAVRIIHLPTNIKVEMQEERTQQKNRDKAMKIIRARVADHFAQIAQDEQDAERKSTVGTGDRSERIRTYNFPQNRVTD
HRIGLTLQKLDSILSGKLDEVIDALILYDQTQKLEELNK
1
359
1ZBT
1
359
Q8DU64
A
1
13
371
1
expression tag
MET
-11
1ZBT
A
Q8DU64
UNP
1
1
expression tag
GLY
-10
1ZBT
A
Q8DU64
UNP
2
1
expression tag
SER
-9
1ZBT
A
Q8DU64
UNP
3
1
expression tag
ASP
-8
1ZBT
A
Q8DU64
UNP
4
1
expression tag
LYS
-7
1ZBT
A
Q8DU64
UNP
5
1
expression tag
ILE
-6
1ZBT
A
Q8DU64
UNP
6
1
expression tag
HIS
-5
1ZBT
A
Q8DU64
UNP
7
1
expression tag
HIS
-4
1ZBT
A
Q8DU64
UNP
8
1
expression tag
HIS
-3
1ZBT
A
Q8DU64
UNP
9
1
expression tag
HIS
-2
1ZBT
A
Q8DU64
UNP
10
1
expression tag
HIS
-1
1ZBT
A
Q8DU64
UNP
11
1
expression tag
HIS
0
1ZBT
A
Q8DU64
UNP
12
1
MET
modified residue
MSE
1
1ZBT
A
Q8DU64
UNP
1
13
1
MET
modified residue
MSE
34
1ZBT
A
Q8DU64
UNP
34
46
1
MET
modified residue
MSE
66
1ZBT
A
Q8DU64
UNP
66
78
1
MET
modified residue
MSE
79
1ZBT
A
Q8DU64
UNP
79
91
1
MET
modified residue
MSE
136
1ZBT
A
Q8DU64
UNP
136
148
1
MET
modified residue
MSE
151
1ZBT
A
Q8DU64
UNP
151
163
1
MET
modified residue
MSE
167
1ZBT
A
Q8DU64
UNP
167
179
1
MET
modified residue
MSE
208
1ZBT
A
Q8DU64
UNP
208
220
1
MET
modified residue
MSE
258
1ZBT
A
Q8DU64
UNP
258
270
1
MET
modified residue
MSE
272
1ZBT
A
Q8DU64
UNP
272
284
8
3
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LYS
147
A
LYS
159
A
ALA
155
A
ALA
167
A
LEU
161
A
LEU
173
A
SER
169
A
SER
181
A
ILE
113
A
ILE
125
A
GLY
119
A
GLY
131
A
HIS
199
A
HIS
211
A
PRO
209
A
PRO
221
A
GLY
182
A
GLY
194
A
ARG
188
A
ARG
200
A
ARG
307
A
ARG
319
A
ASN
312
A
ASN
324
A
ARG
317
A
ARG
329
A
ASP
320
A
ASP
332
A
LEU
325
A
LEU
337
A
LEU
327
A
LEU
339
A
LEU
223
A
LEU
235
A
TYR
228
A
TYR
240
A
ALA
244
A
ALA
256
A
HIS
249
A
HIS
261
A
ILE
254
A
ILE
266
A
MSE
258
A
MSE
270
96
P 43 21 2