0.01195
0.00690
0.00000
0.00000
0.01380
0.00000
0.00000
0.00000
0.02787
0.00000
0.00000
0.00000
Meinke, G.
Bullock, P.A.
Bohm, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
83.669
83.669
35.880
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
C6 H5 O7 -3
189.100
CITRATE ANION
non-polymer
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
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
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
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
C
N
89
N
C
N
90
N
C
N
91
N
C
N
92
N
C
N
93
N
C
N
94
N
O
N
95
N
O
N
96
N
O
N
97
N
O
N
98
N
O
N
99
N
O
N
100
N
O
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
N
N
107
S
C
N
108
N
C
N
109
N
O
N
110
N
C
N
111
N
C
N
112
N
C
N
113
N
O
N
114
N
N
N
115
N
O
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
H
N
124
N
H
N
125
N
H
N
126
N
N
N
127
S
C
N
128
N
C
N
129
N
O
N
130
N
C
N
131
N
C
N
132
N
C
N
133
N
O
N
134
N
O
N
135
N
O
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
N
N
146
N
C
N
147
N
C
N
148
N
O
N
149
N
O
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
N
N
156
S
C
N
157
N
C
N
158
N
O
N
159
N
C
Y
160
N
C
Y
161
N
N
Y
162
N
C
Y
163
N
C
Y
164
N
N
N
165
N
O
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
O
N
177
N
H
N
178
N
H
N
179
N
N
N
180
S
C
N
181
N
C
N
182
N
O
N
183
S
C
N
184
N
C
N
185
N
C
N
186
N
C
N
187
N
O
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
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
N
N
202
S
C
N
203
N
C
N
204
N
O
N
205
N
C
N
206
N
C
N
207
N
C
N
208
N
C
N
209
N
O
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
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
H
N
223
N
N
N
224
S
C
N
225
N
C
N
226
N
O
N
227
N
C
N
228
N
C
N
229
N
C
N
230
N
C
N
231
N
N
N
232
N
O
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
H
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
N
N
249
S
C
N
250
N
C
N
251
N
O
N
252
N
C
N
253
N
C
N
254
N
S
N
255
N
C
N
256
N
O
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
H
N
267
N
H
N
268
N
N
N
269
S
C
N
270
N
C
N
271
N
O
N
272
N
O
N
273
N
C
N
274
N
C
N
275
N
SE
N
276
N
C
N
277
N
H
N
278
N
H
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
N
N
289
S
C
N
290
N
C
N
291
N
O
N
292
N
C
Y
293
N
C
Y
294
N
C
Y
295
N
C
Y
296
N
C
Y
297
N
C
Y
298
N
C
N
299
N
O
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
309
N
H
N
310
N
H
N
311
N
N
N
312
S
C
N
313
N
C
N
314
N
O
N
315
N
C
N
316
N
C
N
317
N
C
N
318
N
O
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
N
N
329
S
C
N
330
N
C
N
331
N
O
N
332
N
C
N
333
N
O
N
334
N
O
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
N
N
343
S
C
N
344
N
C
N
345
N
O
N
346
R
C
N
347
N
O
N
348
N
C
N
349
N
O
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
N
N
360
S
C
N
361
N
C
N
362
N
O
N
363
N
C
Y
364
N
C
Y
365
N
C
Y
366
N
C
Y
367
N
C
Y
368
N
C
Y
369
N
C
N
370
N
O
N
371
N
O
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
N
N
384
S
C
N
385
N
C
N
386
N
O
N
387
N
C
N
388
N
C
N
389
N
C
N
390
N
O
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
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
doub
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
doub
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
doub
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
doub
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
sing
N
123
N
sing
N
124
N
sing
N
125
N
doub
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
doub
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
doub
N
144
N
sing
N
145
N
sing
N
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
doub
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
Y
157
N
sing
Y
158
N
doub
Y
159
N
doub
N
160
N
sing
Y
161
N
sing
N
162
N
sing
Y
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
doub
N
176
N
sing
N
177
N
sing
N
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
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
doub
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
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
doub
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
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
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
doub
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
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
doub
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
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
doub
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
Y
284
N
doub
Y
285
N
sing
Y
286
N
sing
N
287
N
sing
Y
288
N
doub
N
289
N
sing
Y
290
N
doub
N
291
N
sing
Y
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
doub
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
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
doub
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
doub
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
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
doub
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
sing
Y
353
N
doub
Y
354
N
sing
Y
355
N
sing
N
356
N
sing
Y
357
N
doub
N
358
N
sing
Y
359
N
doub
N
360
N
sing
Y
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
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
doub
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
US
J.Virol.
JOVIAM
0825
0022-538X
80
4304
4312
10.1128/JVI.80.9.4304-4312.2006
16611889
Crystal structure of the simian virus 40 large T-antigen origin-binding domain.
2006
10.2210/pdb2fuf/pdb
pdb_00002fuf
100
1
crystal
CCD
2005-03-07
ADSC QUANTUM 315
double crystal
SINGLE WAVELENGTH
M
x-ray
1
0.9793
1.0
12.10
275942
0.070
2.05
1.450
50.000
25306
98.70
10.90
X29A
NSLS
0.9793
SYNCHROTRON
NSLS BEAMLINE X29A
15508.424
Large T antigen
DNA binding domain (residues 131-259)
1
man
polymer
189.100
CITRATE ANION
1
syn
non-polymer
18.015
water
170
nat
water
no
yes
GSKVEDPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKI(MSE)EKYSVTFISRHNSYNHNILFFLTPHRHR
VSAINNYAQKLCTFSFLICKGVNKEYL(MSE)YSALTRDPFSVIEESLPGGLKEHDFNPESS
GSKVEDPKDFPSELLSFLSHAVFSNRTLACFAIYTTKEKAALLYKKIMEKYSVTFISRHNSYNHNILFFLTPHRHRVSAI
NNYAQKLCTFSFLICKGVNKEYLMYSALTRDPFSVIEESLPGGLKEHDFNPESS
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
Polyomavirus
Escherichia
Escherichia coli
sample
SV40 A GENE
10633
Simian virus 40
511693
Escherichia coli BL21
BL21
PLASMID
pGEX-1lT
1
2.34
47.36
VAPOR DIFFUSION, HANGING DROP
6.7
1.6 M Sodium citrate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
298
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
repository
Initial release
Version format compliance
Advisory
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
Refinement description
Data collection
1
0
2006-08-22
1
1
2008-05-01
1
2
2011-07-13
1
3
2017-10-18
1
4
2023-08-30
1
5
2023-11-15
_software.classification
_software.contact_author
_software.contact_author_email
_software.date
_software.language
_software.location
_software.name
_software.type
_software.version
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_chem_comp_atom.atom_id
_chem_comp_bond.atom_id_2
NMR structure of same protein
RCSB
Y
RCSB
2006-01-26
REL
REL
0.050
5.181
2652
99.60
10.90
0.064
3.604
2581
99.70
10.60
0.074
2.912
2545
99.50
11.00
0.084
2.179
2538
99.00
11.10
0.107
1.569
2550
99.20
11.20
0.142
1.202
2505
98.90
11.20
0.193
1.024
2516
98.60
11.20
0.260
0.927
2513
98.30
11.20
0.343
0.835
2490
97.60
10.90
0.441
0.790
2416
96.30
9.70
FLC
CITRATE ANION
HOH
water
1TBD
PDB
experimental model
FLC
200
2
FLC
FLC
263
A
HOH
1
3
HOH
HOH
264
A
HOH
2
3
HOH
HOH
265
A
HOH
3
3
HOH
HOH
266
A
HOH
4
3
HOH
HOH
267
A
HOH
5
3
HOH
HOH
268
A
HOH
6
3
HOH
HOH
269
A
HOH
7
3
HOH
HOH
270
A
HOH
8
3
HOH
HOH
271
A
HOH
9
3
HOH
HOH
272
A
HOH
10
3
HOH
HOH
273
A
HOH
11
3
HOH
HOH
274
A
HOH
12
3
HOH
HOH
275
A
HOH
13
3
HOH
HOH
276
A
HOH
14
3
HOH
HOH
277
A
HOH
15
3
HOH
HOH
278
A
HOH
16
3
HOH
HOH
279
A
HOH
17
3
HOH
HOH
280
A
HOH
18
3
HOH
HOH
281
A
HOH
19
3
HOH
HOH
282
A
HOH
20
3
HOH
HOH
283
A
HOH
21
3
HOH
HOH
284
A
HOH
22
3
HOH
HOH
285
A
HOH
23
3
HOH
HOH
286
A
HOH
24
3
HOH
HOH
287
A
HOH
25
3
HOH
HOH
288
A
HOH
26
3
HOH
HOH
289
A
HOH
27
3
HOH
HOH
290
A
HOH
28
3
HOH
HOH
291
A
HOH
29
3
HOH
HOH
292
A
HOH
30
3
HOH
HOH
293
A
HOH
31
3
HOH
HOH
294
A
HOH
32
3
HOH
HOH
295
A
HOH
33
3
HOH
HOH
296
A
HOH
34
3
HOH
HOH
297
A
HOH
35
3
HOH
HOH
298
A
HOH
36
3
HOH
HOH
299
A
HOH
37
3
HOH
HOH
300
A
HOH
38
3
HOH
HOH
301
A
HOH
39
3
HOH
HOH
302
A
HOH
40
3
HOH
HOH
303
A
HOH
41
3
HOH
HOH
304
A
HOH
42
3
HOH
HOH
305
A
HOH
43
3
HOH
HOH
306
A
HOH
44
3
HOH
HOH
307
A
HOH
45
3
HOH
HOH
308
A
HOH
46
3
HOH
HOH
309
A
HOH
47
3
HOH
HOH
310
A
HOH
48
3
HOH
HOH
311
A
HOH
49
3
HOH
HOH
312
A
HOH
50
3
HOH
HOH
313
A
HOH
51
3
HOH
HOH
314
A
HOH
52
3
HOH
HOH
315
A
HOH
53
3
HOH
HOH
316
A
HOH
54
3
HOH
HOH
317
A
HOH
55
3
HOH
HOH
318
A
HOH
56
3
HOH
HOH
319
A
HOH
57
3
HOH
HOH
320
A
HOH
58
3
HOH
HOH
321
A
HOH
59
3
HOH
HOH
322
A
HOH
60
3
HOH
HOH
323
A
HOH
61
3
HOH
HOH
324
A
HOH
62
3
HOH
HOH
325
A
HOH
63
3
HOH
HOH
326
A
HOH
64
3
HOH
HOH
327
A
HOH
65
3
HOH
HOH
328
A
HOH
66
3
HOH
HOH
329
A
HOH
67
3
HOH
HOH
330
A
HOH
68
3
HOH
HOH
331
A
HOH
69
3
HOH
HOH
332
A
HOH
70
3
HOH
HOH
333
A
HOH
71
3
HOH
HOH
334
A
HOH
72
3
HOH
HOH
335
A
HOH
73
3
HOH
HOH
336
A
HOH
74
3
HOH
HOH
337
A
HOH
75
3
HOH
HOH
338
A
HOH
76
3
HOH
HOH
339
A
HOH
77
3
HOH
HOH
340
A
HOH
78
3
HOH
HOH
341
A
HOH
79
3
HOH
HOH
342
A
HOH
80
3
HOH
HOH
343
A
HOH
81
3
HOH
HOH
344
A
HOH
82
3
HOH
HOH
345
A
HOH
83
3
HOH
HOH
346
A
HOH
84
3
HOH
HOH
347
A
HOH
85
3
HOH
HOH
348
A
HOH
86
3
HOH
HOH
349
A
HOH
87
3
HOH
HOH
350
A
HOH
88
3
HOH
HOH
351
A
HOH
89
3
HOH
HOH
352
A
HOH
90
3
HOH
HOH
353
A
HOH
91
3
HOH
HOH
354
A
HOH
92
3
HOH
HOH
355
A
HOH
93
3
HOH
HOH
356
A
HOH
94
3
HOH
HOH
357
A
HOH
95
3
HOH
HOH
358
A
HOH
96
3
HOH
HOH
359
A
HOH
97
3
HOH
HOH
360
A
HOH
98
3
HOH
HOH
361
A
HOH
99
3
HOH
HOH
362
A
HOH
100
3
HOH
HOH
363
A
HOH
101
3
HOH
HOH
364
A
HOH
102
3
HOH
HOH
365
A
HOH
103
3
HOH
HOH
366
A
HOH
104
3
HOH
HOH
367
A
HOH
105
3
HOH
HOH
368
A
HOH
106
3
HOH
HOH
369
A
HOH
107
3
HOH
HOH
370
A
HOH
108
3
HOH
HOH
371
A
HOH
109
3
HOH
HOH
372
A
HOH
110
3
HOH
HOH
373
A
HOH
111
3
HOH
HOH
374
A
HOH
112
3
HOH
HOH
375
A
HOH
113
3
HOH
HOH
376
A
HOH
114
3
HOH
HOH
377
A
HOH
115
3
HOH
HOH
378
A
HOH
116
3
HOH
HOH
379
A
HOH
117
3
HOH
HOH
380
A
HOH
118
3
HOH
HOH
381
A
HOH
119
3
HOH
HOH
382
A
HOH
120
3
HOH
HOH
383
A
HOH
121
3
HOH
HOH
384
A
HOH
122
3
HOH
HOH
385
A
HOH
123
3
HOH
HOH
386
A
HOH
124
3
HOH
HOH
387
A
HOH
125
3
HOH
HOH
388
A
HOH
126
3
HOH
HOH
389
A
HOH
127
3
HOH
HOH
390
A
HOH
128
3
HOH
HOH
391
A
HOH
129
3
HOH
HOH
392
A
HOH
130
3
HOH
HOH
393
A
HOH
131
3
HOH
HOH
394
A
HOH
132
3
HOH
HOH
395
A
HOH
133
3
HOH
HOH
396
A
HOH
134
3
HOH
HOH
397
A
HOH
135
3
HOH
HOH
398
A
HOH
136
3
HOH
HOH
399
A
HOH
137
3
HOH
HOH
400
A
HOH
138
3
HOH
HOH
401
A
HOH
139
3
HOH
HOH
402
A
HOH
140
3
HOH
HOH
403
A
HOH
141
3
HOH
HOH
404
A
HOH
142
3
HOH
HOH
405
A
HOH
143
3
HOH
HOH
406
A
HOH
144
3
HOH
HOH
407
A
HOH
145
3
HOH
HOH
408
A
HOH
146
3
HOH
HOH
409
A
HOH
147
3
HOH
HOH
410
A
HOH
148
3
HOH
HOH
411
A
HOH
149
3
HOH
HOH
412
A
HOH
150
3
HOH
HOH
413
A
HOH
151
3
HOH
HOH
414
A
HOH
152
3
HOH
HOH
415
A
HOH
153
3
HOH
HOH
416
A
HOH
154
3
HOH
HOH
417
A
HOH
155
3
HOH
HOH
418
A
HOH
156
3
HOH
HOH
419
A
HOH
157
3
HOH
HOH
420
A
HOH
158
3
HOH
HOH
421
A
HOH
159
3
HOH
HOH
422
A
HOH
160
3
HOH
HOH
423
A
HOH
161
3
HOH
HOH
424
A
HOH
162
3
HOH
HOH
425
A
HOH
163
3
HOH
HOH
426
A
HOH
164
3
HOH
HOH
427
A
HOH
165
3
HOH
HOH
428
A
HOH
166
3
HOH
HOH
429
A
HOH
167
3
HOH
HOH
430
A
HOH
168
3
HOH
HOH
431
A
HOH
169
3
HOH
HOH
432
A
HOH
170
3
HOH
HOH
433
A
Se
9.544
0.594
0.029
0.006
1.647
Se
23.852
0.701
0.819
0.146
2.430
0.480
251
0.530
430
0.530
536
0.550
628
0.560
713
0.560
783
0.570
837
0.570
916
0.830
0.850
0.620
5094
4596
498
0.880
0.920
0.750
224
169
55
0.880
0.910
0.690
697
599
98
0.900
0.920
0.700
854
764
90
0.860
0.880
0.650
864
789
75
0.790
0.810
0.510
1502
1386
116
0.730
0.750
0.480
953
889
64
n
1
129
A
n
2
130
A
LYS
131
n
3
LYS
131
A
VAL
132
n
4
VAL
132
A
GLU
133
n
5
GLU
133
A
ASP
134
n
6
ASP
134
A
PRO
135
n
7
PRO
135
A
LYS
136
n
8
LYS
136
A
ASP
137
n
9
ASP
137
A
PHE
138
n
10
PHE
138
A
PRO
139
n
11
PRO
139
A
SER
140
n
12
SER
140
A
GLU
141
n
13
GLU
141
A
LEU
142
n
14
LEU
142
A
LEU
143
n
15
LEU
143
A
SER
144
n
16
SER
144
A
PHE
145
n
17
PHE
145
A
LEU
146
n
18
LEU
146
A
SER
147
n
19
SER
147
A
HIS
148
n
20
HIS
148
A
ALA
149
n
21
ALA
149
A
VAL
150
n
22
VAL
150
A
PHE
151
n
23
PHE
151
A
SER
152
n
24
SER
152
A
ASN
153
n
25
ASN
153
A
ARG
154
n
26
ARG
154
A
THR
155
n
27
THR
155
A
LEU
156
n
28
LEU
156
A
ALA
157
n
29
ALA
157
A
CYS
158
n
30
CYS
158
A
PHE
159
n
31
PHE
159
A
ALA
160
n
32
ALA
160
A
ILE
161
n
33
ILE
161
A
TYR
162
n
34
TYR
162
A
THR
163
n
35
THR
163
A
THR
164
n
36
THR
164
A
LYS
165
n
37
LYS
165
A
GLU
166
n
38
GLU
166
A
LYS
167
n
39
LYS
167
A
ALA
168
n
40
ALA
168
A
ALA
169
n
41
ALA
169
A
LEU
170
n
42
LEU
170
A
LEU
171
n
43
LEU
171
A
TYR
172
n
44
TYR
172
A
LYS
173
n
45
LYS
173
A
LYS
174
n
46
LYS
174
A
ILE
175
n
47
ILE
175
A
MSE
176
n
48
MSE
176
A
GLU
177
n
49
GLU
177
A
LYS
178
n
50
LYS
178
A
TYR
179
n
51
TYR
179
A
SER
180
n
52
SER
180
A
VAL
181
n
53
VAL
181
A
THR
182
n
54
THR
182
A
PHE
183
n
55
PHE
183
A
ILE
184
n
56
ILE
184
A
SER
185
n
57
SER
185
A
ARG
186
n
58
ARG
186
A
HIS
187
n
59
HIS
187
A
ASN
188
n
60
ASN
188
A
SER
189
n
61
SER
189
A
TYR
190
n
62
TYR
190
A
ASN
191
n
63
ASN
191
A
HIS
192
n
64
HIS
192
A
ASN
193
n
65
ASN
193
A
ILE
194
n
66
ILE
194
A
LEU
195
n
67
LEU
195
A
PHE
196
n
68
PHE
196
A
PHE
197
n
69
PHE
197
A
LEU
198
n
70
LEU
198
A
THR
199
n
71
THR
199
A
PRO
200
n
72
PRO
200
A
HIS
201
n
73
HIS
201
A
ARG
202
n
74
ARG
202
A
HIS
203
n
75
HIS
203
A
ARG
204
n
76
ARG
204
A
VAL
205
n
77
VAL
205
A
SER
206
n
78
SER
206
A
ALA
207
n
79
ALA
207
A
ILE
208
n
80
ILE
208
A
ASN
209
n
81
ASN
209
A
ASN
210
n
82
ASN
210
A
TYR
211
n
83
TYR
211
A
ALA
212
n
84
ALA
212
A
GLN
213
n
85
GLN
213
A
LYS
214
n
86
LYS
214
A
LEU
215
n
87
LEU
215
A
CYS
216
n
88
CYS
216
A
THR
217
n
89
THR
217
A
PHE
218
n
90
PHE
218
A
SER
219
n
91
SER
219
A
PHE
220
n
92
PHE
220
A
LEU
221
n
93
LEU
221
A
ILE
222
n
94
ILE
222
A
CYS
223
n
95
CYS
223
A
LYS
224
n
96
LYS
224
A
GLY
225
n
97
GLY
225
A
VAL
226
n
98
VAL
226
A
ASN
227
n
99
ASN
227
A
LYS
228
n
100
LYS
228
A
GLU
229
n
101
GLU
229
A
TYR
230
n
102
TYR
230
A
LEU
231
n
103
LEU
231
A
MSE
232
n
104
MSE
232
A
TYR
233
n
105
TYR
233
A
SER
234
n
106
SER
234
A
ALA
235
n
107
ALA
235
A
LEU
236
n
108
LEU
236
A
THR
237
n
109
THR
237
A
ARG
238
n
110
ARG
238
A
ASP
239
n
111
ASP
239
A
PRO
240
n
112
PRO
240
A
PHE
241
n
113
PHE
241
A
SER
242
n
114
SER
242
A
VAL
243
n
115
VAL
243
A
ILE
244
n
116
ILE
244
A
GLU
245
n
117
GLU
245
A
GLU
246
n
118
GLU
246
A
SER
247
n
119
SER
247
A
LEU
248
n
120
LEU
248
A
PRO
249
n
121
PRO
249
A
GLY
250
n
122
GLY
250
A
GLY
251
n
123
GLY
251
A
LEU
252
n
124
LEU
252
A
LYS
253
n
125
LYS
253
A
GLU
254
n
126
GLU
254
A
HIS
255
n
127
HIS
255
A
ASP
256
n
128
ASP
256
A
n
129
257
A
n
130
258
A
n
131
259
A
n
132
260
A
n
133
261
A
n
134
262
A
1.2810
-0.0872
0.2714
0.8212
-0.0407
0.8451
0.0186
0.0698
-0.0130
-0.0091
0.0421
-0.0080
-0.0298
-0.0374
-0.0607
-0.0510
0.0012
0.0011
-0.0302
-0.0087
-0.0179
refined
12.6360
72.1600
0.8010
X-RAY DIFFRACTION
A
131
A
3
A
256
A
128
X-RAY DIFFRACTION
1
ALL
author_defined_assembly
6
hexameric
A
MSE
176
SELENOMETHIONINE
A
MSE
48
MET
A
MSE
232
SELENOMETHIONINE
A
MSE
104
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
0.5000000000
-0.8660254038
0.0000000000
0.8660254038
0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
6_655
x-y+1,x,z+5/6
crystal symmetry operation
83.6690000000
0.0000000000
29.9000000000
-0.5000000000
-0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_765
-y+2,x-y+1,z+2/3
crystal symmetry operation
125.5035000000
72.4594795092
23.9200000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
4_775
-x+2,-y+2,z+1/2
crystal symmetry operation
83.6690000000
144.9189590185
17.9400000000
-0.5000000000
0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
3_675
-x+y+1,-x+2,z+1/3
crystal symmetry operation
0.0000000000
144.9189590185
11.9600000000
0.5000000000
0.8660254038
0.0000000000
-0.8660254038
0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
5_565
y,-x+y+1,z+1/6
crystal symmetry operation
-41.8345000000
72.4594795092
5.9800000000
A
O
ILE
222
A
O
ILE
94
A
N
TYR
162
A
N
TYR
34
A
N
LEU
156
A
N
LEU
28
A
O
HIS
203
A
O
HIS
75
A
O
PHE
196
A
O
PHE
68
A
N
SER
185
A
N
SER
57
A
N
ARG
186
A
N
ARG
58
A
O
ILE
244
A
O
ILE
116
1
A
GLY
129
A
GLY
1
1
Y
1
A
SER
130
A
SER
2
1
Y
1
A
PHE
257
A
PHE
129
1
Y
1
A
ASN
258
A
ASN
130
1
Y
1
A
PRO
259
A
PRO
131
1
Y
1
A
GLU
260
A
GLU
132
1
Y
1
A
SER
261
A
SER
133
1
Y
1
A
SER
262
A
SER
134
1
Y
1
A
HIS
192
-119.11
-167.41
1
A
ASP
239
B
-29.69
125.98
2.50
30.00
0.550
5094
19.648
-0.200
-0.100
0.000
-0.200
0.000
0.300
0.966
0.959
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.189
0.169
0.17
0.17
1.450
50
1252
25306
24796
4.900
98.740
1.905
0.037
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
0.00
0.00
SAD
0.065
0.064
0.800
0.800
1.200
1TBD
MAXIMUM LIKELIHOOD
MASK
1.450
50
170
1212
13
0
1029
0.008
0.022
1143
1.141
1.961
1558
6.000
5.000
144
29.999
23.265
49
12.112
15.000
205
7.742
15.000
5
0.082
0.200
170
0.005
0.020
879
0.199
0.200
554
0.307
0.200
820
0.096
0.200
138
0.212
0.200
68
0.151
0.200
21
0.716
1.500
705
1.195
2.000
1127
1.791
3.000
489
2.671
4.500
429
0.27
0.205
1.488
91
1707
1798
20
96.000
23.3
1.450
50.000
2FUF
25306
24796
0
0
0.07
0.07
2.052
1
53.6
10.900
98.700
0.441
1.45
1.50
4.5
2416
2416
0.441
0.790
1
9.70
96.3
96.30
data reduction
Zbyszek Otwinowski
zbyszek@mix.swmed.edu
http://www.lnls.br/infra/linhasluz/denzo-hkl.htm
DENZO
package
data scaling
Zbyszek Otwinowski
zbyszek@mix.swmed.edu
http://www.lnls.br/infra/linhasluz/denzo-hkl.htm
SCALEPACK
package
phasing
R. J. Read
cimr-phaser@lists.cam.ac.uk
http://www-structmed.cimr.cam.ac.uk/phaser/
PHASER
program
phasing
Tom Terwilliger
terwilliger@LANL.gov
14-Sept-2004
http://www.solve.lanl.gov/
SOLVE
program
2.08
phasing
Terwilliger, T. C
terwilliger@LANL.gov
14-Sept-2004
http://www.solve.lanl.gov/
RESOLVE
program
2.08
refinement
Murshudov, G.N.
ccp4@dl.ac.uk
Fortran
http://www.ccp4.ac.uk/main.html
REFMAC
program
data extraction
PDB
sw-help@rcsb.rutgers.edu
Nov. 1, 2005
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
1.701
Crystal structure of the SV40 large T antigen origin-binding domain
1
N
N
2
N
N
3
N
N
The biological assembly is a hexamer generated from the monomer
in the asymmetric unit by the operations:y,-x+y+1,z+1/6 and -x+y+1,-x+2,z+1/3 and -x+2,-y+2,z+1/2, and -y+2,x-y+1,z+2/3 and x-y+1,x,z+5/6
A
PRO
139
A
PRO
11
HELX_P
A
LEU
146
A
LEU
18
5
1
8
A
THR
164
A
THR
36
HELX_P
A
TYR
179
A
TYR
51
1
2
16
A
ARG
204
A
ARG
76
HELX_P
A
CYS
216
A
CYS
88
1
3
13
A
LYS
228
A
LYS
100
HELX_P
A
THR
237
A
THR
109
1
4
10
A
GLY
250
A
GLY
122
HELX_P
A
HIS
255
A
HIS
127
1
5
6
covale
1.331
both
A
ILE
175
A
C
ILE
47
1_555
A
MSE
176
A
N
MSE
48
1_555
covale
1.325
both
A
MSE
176
A
C
MSE
48
1_555
A
GLU
177
A
N
GLU
49
1_555
covale
1.332
both
A
LEU
231
A
C
LEU
103
1_555
A
MSE
232
A
N
MSE
104
1_555
covale
1.331
both
A
MSE
232
A
C
MSE
104
1_555
A
TYR
233
A
N
TYR
105
1_555
DNA BINDING PROTEIN
Replication origin binding domain, dna replication, DNA BINDING PROTEIN
A
ASP
239
A
ASP
111
1
A
PRO
240
A
PRO
112
6.92
A
ASP
239
A
ASP
111
1
A
PRO
240
A
PRO
112
4.75
TALA_SV40
UNP
1
131
P03070
131
260
2FUF
131
259
P03070
A
1
3
131
1
cloning artifact
GLY
129
2FUF
A
P03070
UNP
1
1
cloning artifact
SER
130
2FUF
A
P03070
UNP
2
1
MET
modified residue
MSE
176
2FUF
A
P03070
UNP
176
48
1
MET
modified residue
MSE
232
2FUF
A
P03070
UNP
232
104
1
cloning artifact
SER
261
2FUF
A
P03070
UNP
133
1
cloning artifact
SER
262
2FUF
A
P03070
UNP
134
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LEU
221
A
LEU
93
A
GLY
225
A
GLY
97
A
LEU
156
A
LEU
28
A
THR
163
A
THR
35
A
HIS
192
A
HIS
64
A
HIS
203
A
HIS
75
A
PHE
183
A
PHE
55
A
SER
189
A
SER
61
A
SER
242
A
SER
114
A
GLU
246
A
GLU
118
BINDING SITE FOR RESIDUE FLC A 263
A
FLC
263
Software
9
A
THR
164
A
THR
36
9
1_555
A
LYS
165
A
LYS
37
9
1_555
A
ASN
191
A
ASN
63
9
1_555
A
HIS
192
A
HIS
64
9
1_555
A
ARG
238
A
ARG
110
9
4_674
A
HOH
281
C
HOH
9
1_555
A
HOH
305
C
HOH
9
1_555
A
HOH
334
C
HOH
9
4_674
A
HOH
391
C
HOH
9
1_555
170
P 65