1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Marvin, D.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C3 H7 N O2
89.093
y
ALANINE
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 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
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
O
N
21
N
O
N
22
N
O
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
N
N
31
S
C
N
32
N
C
N
33
N
O
N
34
N
C
N
35
N
C
N
36
N
C
N
37
N
O
N
38
N
N
N
39
N
O
N
40
N
H
N
41
N
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
N
N
51
S
C
N
52
N
C
N
53
N
O
N
54
N
C
N
55
N
C
N
56
N
C
N
57
N
O
N
58
N
O
N
59
N
O
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
N
N
70
N
C
N
71
N
C
N
72
N
O
N
73
N
O
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
N
N
80
S
C
N
81
N
C
N
82
N
O
N
83
S
C
N
84
N
C
N
85
N
C
N
86
N
C
N
87
N
O
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
N
N
102
S
C
N
103
N
C
N
104
N
O
N
105
N
C
N
106
N
C
N
107
N
C
N
108
N
C
N
109
N
O
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
N
N
124
S
C
N
125
N
C
N
126
N
O
N
127
N
C
N
128
N
C
N
129
N
C
N
130
N
C
N
131
N
N
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
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
N
N
149
S
C
N
150
N
C
N
151
N
O
N
152
N
C
N
153
N
C
N
154
N
S
N
155
N
C
N
156
N
O
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
N
N
169
S
C
N
170
N
C
N
171
N
O
N
172
N
C
Y
173
N
C
Y
174
N
C
Y
175
N
C
Y
176
N
C
Y
177
N
C
Y
178
N
C
N
179
N
O
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
N
N
192
S
C
N
193
N
C
N
194
N
O
N
195
N
C
N
196
N
C
N
197
N
C
N
198
N
O
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
H
N
207
N
H
N
208
N
N
N
209
S
C
N
210
N
C
N
211
N
O
N
212
N
C
N
213
N
O
N
214
N
O
N
215
N
H
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
N
N
223
S
C
N
224
N
C
N
225
N
O
N
226
R
C
N
227
N
O
N
228
N
C
N
229
N
O
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
N
N
240
S
C
N
241
N
C
N
242
N
O
N
243
N
C
Y
244
N
C
Y
245
N
C
Y
246
N
C
Y
247
N
N
Y
248
N
C
Y
249
N
C
Y
250
N
C
Y
251
N
C
Y
252
N
C
N
253
N
O
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
N
N
267
S
C
N
268
N
C
N
269
N
O
N
270
N
C
Y
271
N
C
Y
272
N
C
Y
273
N
C
Y
274
N
C
Y
275
N
C
Y
276
N
C
N
277
N
O
N
278
N
O
N
279
N
H
N
280
N
H
N
281
N
H
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
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
N
C
N
295
N
C
N
296
N
C
N
297
N
O
N
298
N
H
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
H
N
307
N
H
N
308
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
doub
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
sing
N
34
N
doub
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
doub
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
doub
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
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
doub
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
doub
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
sing
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
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
doub
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
sing
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
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
doub
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
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
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
doub
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
sing
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
doub
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
Y
170
N
doub
Y
171
N
sing
Y
172
N
sing
N
173
N
sing
Y
174
N
doub
N
175
N
sing
Y
176
N
doub
N
177
N
sing
Y
178
N
sing
N
179
N
sing
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
doub
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
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
doub
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
doub
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
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
doub
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
Y
239
N
doub
Y
240
N
sing
Y
241
N
sing
N
242
N
sing
Y
243
N
doub
Y
244
N
sing
Y
245
N
sing
N
246
N
sing
Y
247
N
sing
Y
248
N
doub
N
249
N
sing
Y
250
N
doub
N
251
N
sing
Y
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
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
doub
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
Y
267
N
doub
Y
268
N
sing
Y
269
N
sing
N
270
N
sing
Y
271
N
doub
N
272
N
sing
Y
273
N
doub
N
274
N
sing
Y
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
sing
N
284
N
sing
N
285
N
sing
N
286
N
doub
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
sing
N
297
N
sing
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IJBMDR
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0141-8130
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10.1016/0141-8130(90)90064-H
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JMOBAK
0070
0022-2836
88
581
Filamentous Bacterial Viruses Xii. Molecular Architecture of the Class I (Fd, If1, Ike) Virion
1974
1
2
3
10.2210/pdb1ifd/pdb
pdb_00001ifd
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
1
1.0
5244.000
INOVIRUS
1
man
polymer
no
no
AEGDDPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS
AEGDDPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS
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
Inovirus
Enterobacteria phage M13
sample
10864
Enterobacteria phage fd
BACTERIA
M13
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_status
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Other
1
0
1994-07-31
1
1
2008-03-24
1
2
2011-07-13
1
3
2024-02-07
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.type
Y
BNL
1992-02-16
REL
INOVIRUS STRAIN FD WAS GROWN IN ESCHERICHIA COLI. THERE
ARE TWO SYMMETRY CLASSES OF INOVIRUS. CLASS I INCLUDES
STRAINS FD, IF1 AND IKE. CLASS II INCLUDES STRAINS PF1
AND XF. STRAIN FD BELONGS TO THE FF GROUP WITHIN CLASS I.
THE MEMBERS OF THE FF GROUP HAVE VIRTUALLY IDENTICAL COAT
PROTEIN SEQUENCES AND ONLY SLIGHTLY DIFFERENT GENOME
SEQUENCES. OTHER COMMONLY STUDIED FF STRAINS ARE F1, WHICH
HAS THE SAME COAT PROTEIN SEQUENCE AS FD; AND M13, WHICH
HAS AN ASP TO ASN EXCHANGE AT POSITION 12. THE COORDINATES
OF THE M13 MODEL CAN BE DERIVED BY SUBSTITUTING ASN 12 FOR
ASP 12 IN THE FD MODEL. MEMBERS OF THE FF GROUP GROW IN
ESCHERICHIA COLI BACTERIA THAT CARRY THE F-FACTOR GENES.
SOME OF THESE GENES ARE REQUIRED TO GENERATE THE F-PILI,
WHICH ARE PROTEIN APPENDAGES THAT PROTRUDE FROM THE SURFACE
OF THE BACTERIA AND ARE NECESSARY FOR ADSORPTION OF FD AS
THE FIRST STEP IN INFECTION AND GROWTH.
5
no
1
55
16.000000
-33.230000
ALA
1
n
1
ALA
1
A
GLU
2
n
2
GLU
2
A
GLY
3
n
3
GLY
3
A
ASP
4
n
4
ASP
4
A
ASP
5
n
5
ASP
5
A
PRO
6
n
6
PRO
6
A
ALA
7
n
7
ALA
7
A
LYS
8
n
8
LYS
8
A
ALA
9
n
9
ALA
9
A
ALA
10
n
10
ALA
10
A
PHE
11
n
11
PHE
11
A
ASP
12
n
12
ASP
12
A
SER
13
n
13
SER
13
A
LEU
14
n
14
LEU
14
A
GLN
15
n
15
GLN
15
A
ALA
16
n
16
ALA
16
A
SER
17
n
17
SER
17
A
ALA
18
n
18
ALA
18
A
THR
19
n
19
THR
19
A
GLU
20
n
20
GLU
20
A
TYR
21
n
21
TYR
21
A
ILE
22
n
22
ILE
22
A
GLY
23
n
23
GLY
23
A
TYR
24
n
24
TYR
24
A
ALA
25
n
25
ALA
25
A
TRP
26
n
26
TRP
26
A
ALA
27
n
27
ALA
27
A
MET
28
n
28
MET
28
A
VAL
29
n
29
VAL
29
A
VAL
30
n
30
VAL
30
A
VAL
31
n
31
VAL
31
A
ILE
32
n
32
ILE
32
A
VAL
33
n
33
VAL
33
A
GLY
34
n
34
GLY
34
A
ALA
35
n
35
ALA
35
A
THR
36
n
36
THR
36
A
ILE
37
n
37
ILE
37
A
GLY
38
n
38
GLY
38
A
ILE
39
n
39
ILE
39
A
LYS
40
n
40
LYS
40
A
LEU
41
n
41
LEU
41
A
PHE
42
n
42
PHE
42
A
LYS
43
n
43
LYS
43
A
LYS
44
n
44
LYS
44
A
PHE
45
n
45
PHE
45
A
THR
46
n
46
THR
46
A
SER
47
n
47
SER
47
A
LYS
48
n
48
LYS
48
A
ALA
49
n
49
ALA
49
A
SER
50
n
50
SER
50
A
representative helical assembly
55
helical
helical asymmetric unit
1
monomeric
helical asymmetric unit, std helical frame
1
monomeric
1.00000000
0.00000000
0.00000000
0.00000000
1.00000000
0.00000000
0.00000000
0.00000000
1.00000000
1_555
x,y,z
identity operation
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0.00000
0.00000
-0.97092575
-0.23938084
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0.23938084
-0.97092575
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0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-80.00000
-0.52769727
0.84943251
0.00000000
-0.84943251
-0.52769727
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-80.00000
0.64479090
0.76435901
0.00000000
-0.76435901
0.64479090
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-80.00000
0.92619996
-0.37703267
0.00000000
0.37703267
0.92619996
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-80.00000
-0.07236785
-0.99737801
0.00000000
0.99737801
-0.07236785
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-80.00000
-0.68097653
-0.73230524
0.00000000
0.73230524
-0.68097653
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-64.00000
-0.90689699
0.42135241
0.00000000
-0.42135241
-0.90689699
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-64.00000
0.12048337
0.99271535
0.00000000
-0.99271535
0.12048337
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-64.00000
0.98135981
0.19217942
0.00000000
-0.19217942
0.98135981
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-64.00000
0.48603035
-0.87394193
0.00000000
0.87394193
0.48603035
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
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0.00000
-64.00000
-0.16831734
-0.98573286
0.00000000
0.98573286
-0.16831734
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
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0.00000
-48.00000
-0.98950058
-0.14452890
0.00000000
0.14452890
-0.98950058
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
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0.00000
-48.00000
-0.44322765
0.89640909
0.00000000
-0.89640909
-0.44322765
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-48.00000
0.71557083
0.69854019
0.00000000
-0.69854019
0.71557083
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-48.00000
0.88547474
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0.00000000
0.46468751
0.88547474
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
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-48.00000
0.39938920
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0.00000000
0.91678147
0.39938920
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-32.00000
-0.74849294
-0.66314276
0.00000000
0.66314276
-0.74849294
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-32.00000
-0.86198328
0.50693671
0.00000000
-0.50693671
-0.86198328
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-32.00000
0.21575798
0.97644687
0.00000000
-0.97644687
0.21575798
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-32.00000
0.99532904
0.09654065
0.00000000
-0.09654065
0.99532904
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-32.00000
0.83647750
-0.54800128
0.00000000
0.54800128
0.83647750
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-16.00000
-0.26269442
-0.96487908
0.00000000
0.96487908
-0.26269442
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-16.00000
-0.99883158
-0.04832679
0.00000000
0.04832679
-0.99883158
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-16.00000
-0.35461744
0.93501148
0.00000000
-0.93501148
-0.35461744
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-16.00000
0.77966595
0.62619567
0.00000000
-0.62619567
0.77966595
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
-16.00000
1.00000000
0.00000000
0.00000000
0.00000000
1.00000000
0.00000000
0.00000000
0.00000000
1.00000000
1_555
x,y,z
identity operation
0.00000
0.00000
0.00000
0.30901699
-0.95105652
0.00000000
0.95105652
0.30901699
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
0.00000
-0.80901699
-0.58778525
0.00000000
0.58778525
-0.80901699
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
0.00000
-0.80901699
0.58778525
0.00000000
-0.58778525
-0.80901699
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
0.00000
0.30901699
0.95105652
0.00000000
-0.95105652
0.30901699
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
0.00000
0.83647750
0.54800128
0.00000000
-0.54800128
0.83647750
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
16.00000
0.77966595
-0.62619567
0.00000000
0.62619567
0.77966595
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
16.00000
-0.35461744
-0.93501148
0.00000000
0.93501148
-0.35461744
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
16.00000
-0.99883158
0.04832679
0.00000000
-0.04832679
-0.99883158
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
16.00000
-0.26269442
0.96487908
0.00000000
-0.96487908
-0.26269442
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
16.00000
0.39938920
0.91678147
0.00000000
-0.91678147
0.39938920
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
32.00000
0.99532904
-0.09654065
0.00000000
0.09654065
0.99532904
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
32.00000
0.21575798
-0.97644687
0.00000000
0.97644687
0.21575798
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
32.00000
-0.86198328
-0.50693671
0.00000000
0.50693671
-0.86198328
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
32.00000
-0.74849294
0.66314276
0.00000000
-0.66314276
-0.74849294
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
32.00000
-0.16831734
0.98573286
0.00000000
-0.98573286
-0.16831734
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
48.00000
0.88547474
0.46468751
0.00000000
-0.46468751
0.88547474
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
48.00000
0.71557083
-0.69854019
0.00000000
0.69854019
0.71557083
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
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0.00000
48.00000
-0.44322765
-0.89640909
0.00000000
0.89640909
-0.44322765
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
48.00000
-0.98950058
0.14452890
0.00000000
-0.14452890
-0.98950058
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
48.00000
-0.68097653
0.73230524
0.00000000
-0.73230524
-0.68097653
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
64.00000
0.48603035
0.87394193
0.00000000
-0.87394193
0.48603035
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
64.00000
0.98135981
-0.19217942
0.00000000
0.19217942
0.98135981
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
64.00000
0.12048337
-0.99271535
0.00000000
0.99271535
0.12048337
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
64.00000
-0.90689699
-0.42135241
0.00000000
0.42135241
-0.90689699
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
64.00000
-0.97092575
0.23938084
0.00000000
-0.23938084
-0.97092575
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
80.00000
-0.07236785
0.99737801
0.00000000
-0.99737801
-0.07236785
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
80.00000
0.92619996
0.37703267
0.00000000
-0.37703267
0.92619996
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
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0.00000
80.00000
0.64479090
-0.76435901
0.00000000
0.76435901
0.64479090
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
80.00000
-0.52769727
-0.84943251
0.00000000
0.84943251
-0.52769727
0.00000000
0.00000000
0.00000000
1.00000000
helical symmetry operation
0.00000
0.00000
80.00000
1
A
A
NE1
CE2
TRP
TRP
26
26
-0.093
0.013
1.371
1.278
N
THE MODEL OF THE VIRION HELIX ASYMMETRIC UNIT IS AN
ALPHA-HELIX APPROXIMATION TO THE STRUCTURE, SO THE ENTIRE
MODEL IS ONE STRETCH OF GENTLY-CURVED HELIX. COORDINATES
ARE GIVEN FOR A SINGLE ASYMMETRIC UNIT OF THE COAT PROTEIN
ASSEMBLY. THE COMPLETE PROTEIN ASSEMBLY CONTAINS SEVERAL
THOUSAND ASYMMETRIC UNITS; THE EXACT NUMBER DEPENDS ON THE
LENGTH OF THE DNA. THE PROTEIN ASSEMBLY FORMS A
CYLINDRICAL SHELL SURROUNDING A DNA CORE. THE DNA IS ABOUT
12% BY WEIGHT OF THE FD VIRION, AND PROBABLY HAS NO
WELL-DEFINED STRUCTURE OTHER THAN THAT IMPOSED BY ITS
SINGLE-STRANDED CIRCULAR TOPOLOGY: TWO OPPOSITELY DIRECTED
DNA CHAINS RUN ALONG THE LENGTH OF THE VIRION TO COMPLETE
THE CIRCLE. THE DNA MAY BE A LEFT-HANDED HELIX (SEE JRNL
REFERENCE). THE TWO ENDS OF THE VIRION ARE CAPPED BY A FEW
COPIES OF MINOR COAT PROTEINS, WHOSE STRUCTURE IS NOT
KNOWN. THESE PROTEINS INTERACT WITH THE ENDS OF THE MAJOR
COAT PROTEIN ASSEMBLY. THE N-TERMINAL END OF INOVIRUS HAS
AN OPEN CUP SHAPE, AND THE C-TERMINAL END IS THE COMPLEMENT
OF THIS, A POINTED ARROWHEAD SHAPE (SEE REFERENCES 1 AND
2). THE TWO ENDS OF THE FD ASSEMBLY CAN BE GENERATED BY
OPERATING REPEATEDLY (SAY 10 - 20 TIMES) ON THE HELIX UNIT
CELL CONTENTS (THE GROUP OF 5 ASYMMETRIC UNITS) WITH THE
HELIX PARAMETERS, GIVING TWO DIFFERENT ENDS CONNECTED BY A
SHORT SHAFT. SINCE THE MAJOR COAT PROTEIN SUBUNITS AT THE
ENDS HAVE FEWER NEIGHBORS THAN THOSE IN THE CENTER OF THE
ASSEMBLY, THEIR CONFORMATIONS ARE LESS CONSTRAINED AND MAY
BE MODIFIED BY INTERACTION WITH THE MINOR COAT PROTEINS.
THE HELIX UNIT CELL PARAMETERS ARE AFFECTED BY EXPERIMENTAL
CONDITIONS SUCH AS HYDRATION, PH AND TEMPERATURE. BECAUSE
OF THE OVERLAPPING INTERDIGITATED NATURE OF THE ASSEMBLY,
EVEN SMALL CHANGES IN THE UNIT CELL PARAMETERS ARE
ACCOMPANIED BY CHANGES IN THE SHAPE OF THE ASYMMETRIC UNIT.
THESE CHANGES DO NOT ALTER THE PATTERN OF SIDE CHAIN
INTERLOCKING BETWEEN NEIGHBORING ASYMMETRIC UNITS, BUT THEY
CAN ALTER LOCAL NON-BONDED CONTACTS BY SEVERAL TENTHS OF AN
ANGSTROM. THE DEPOSITORS DEFINE A CANONICAL HELIX UNIT
CELL WITH PARAMETERS T = -33.23 DEGREES, P = 16.0 ANGSTROMS
AND GIVE THE ATOMIC COORDINATES FOR THE ASYMMETRIC UNIT IN
THIS UNIT CELL. TO DETERMINE THE COORDINATES OF THE
ASYMMETRIC UNIT IN A NEW UNIT CELL WITH SLIGHTLY DIFFERENT
PARAMETERS (T', P'), CONVERT FROM CARTESIAN COORDINATES TO
CYLINDRICAL-POLAR COORDINATES AND USE EQUATION 5 OF THE
JRNL REFERENCE. AN EQUIVALENT ALTERNATIVE METHOD IS TO
APPLY A VARIABLE MATRIX THAT IS A FUNCTION OF THE Z
COORDINATE OF THE ATOMS. DEFINE A SLEW COEFFICIENT
S=(T'-T)/P; FOR EXAMPLE, FOR FD AT PH 2, T'=-36.0 DEGREES
DEGREES, P'=16.15 ANGSTROMS AND S=-0.173 DEGREE/ANGSTROM.
THEN, TO GENERATE THE SLEWED COORDINATES, APPLY THE MATRIX
AND VECTOR (RECALCULATED FOR EACH ATOM):
| COS(S*Z) -SIN(S*Z) 0 | | 0 |
| SIN(S*Z) COS(S*Z) 0 | + | 0 |
| 0 0 1 | | (P'/P)*Z |
SLEWING THE COORDINATES IN THIS WAY GIVES RISE TO SMALL
LOCAL DISTORTIONS IN COVALENT BOND LENGTHS AND BOND ANGLES,
WHICH CAN BE CORRECTED BY A FEW CYCLES OF ENERGY
MINIMIZATION.
THE TEMPERATURE FACTOR WAS NOT REFINED AND IS GIVEN THE
ARBITRARY VALUE OF 10.
4.00
1
4.00
0
370
0
0
370
0.004
refinement
EREF
MODEL-BUILDING STUDIES OF INOVIRUS: GENETIC VARIATIONS ON A GEOMETRIC THEME
1
Y
N
A
ALA
1
A
ALA
1
HELX_P
A
SER
50
A
SER
50
1
A
50
VIRUS
VIRUS, Helical virus
COATB_BPFD
UNP
1
1
P69539
MKKSLVLKASVAVATLVPMLSFAAEGDDPAKAAFDSLQASATEYIGYAWAMVVVIVGATIGIKLFKKFTSKAS
24
73
1IFD
1
50
P69539
A
1
1
50
1
P 1