regulation of DNA stability / cellular response to hydroxyurea / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / proteasomal protein catabolic process / regulation of protein stability / aspartic-type endopeptidase activity Similarity search - Function
Resolution: 1.7→28.27 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.285 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19871
1499
5 %
RANDOM
Rwork
0.17573
-
-
-
obs
0.17686
28725
97.65 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 27.812 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.42 Å2
0 Å2
-0.59 Å2
2-
-
0.65 Å2
0 Å2
3-
-
-
-0.59 Å2
Refinement step
Cycle: LAST / Resolution: 1.7→28.27 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1891
0
27
175
2093
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.022
2050
X-RAY DIFFRACTION
r_angle_refined_deg
1.457
1.977
2767
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.303
5
263
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
29.323
23.412
85
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.887
15
384
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.444
15
18
X-RAY DIFFRACTION
r_chiral_restr
0.102
0.2
312
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.021
1510
X-RAY DIFFRACTION
r_mcbond_it
0.757
1.5
1280
X-RAY DIFFRACTION
r_mcangle_it
1.338
2
2071
X-RAY DIFFRACTION
r_scbond_it
2.473
3
770
X-RAY DIFFRACTION
r_scangle_it
3.645
4.5
695
LS refinement shell
Resolution: 1.7→1.744 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.31
88
-
Rwork
0.299
1631
-
obs
-
-
75.83 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
4.7447
0.4756
1.3447
2.028
-0.9232
6.2401
-0.0177
0.0914
0.013
-0.0974
0.1157
0.1177
0.1026
-0.4418
-0.098
0.0765
-0.0117
0.0063
0.0871
-0.0058
0.0886
0.8054
14.6165
-12.6036
2
5.2146
-1.1804
0.6032
4.7153
1.6129
3.6101
0.0018
-0.165
-0.0737
0.1261
0.0578
-0.1359
-0.0673
-0.0682
-0.0596
0.0713
-0.0002
0.0005
0.0808
0.0165
0.0874
10.3694
17.585
1.9939
3
1.5103
0.3172
-2.2992
0.9908
-1.0454
8.2257
-0.0147
0.017
0.0514
-0.0744
0.0637
0.0243
-0.0625
-0.0669
-0.049
0.0677
0.0092
-0.0039
0.0843
-0.0017
0.0906
5.1194
18.9755
-11.4274
4
2.2746
2.5199
5.7776
6.2392
5.4671
15.3287
-0.2812
0.1927
0.0736
-0.4809
0.1371
-0.0101
-0.901
0.4401
0.1441
0.1759
0.0041
0.0269
0.1261
0.029
0.1127
11.1785
26.5081
-15.5835
5
2.9974
1.0101
0.9094
3.0464
-2.1621
4.4453
0.1073
-0.0991
0.0976
0.1251
-0.0158
0.1149
-0.1012
-0.0573
-0.0915
0.0773
0.0003
0.0135
0.0671
-0.0129
0.0934
8.6176
27.1203
1.272
6
3.1556
2.4665
0.8575
6.1655
-0.5106
5.9369
-0.0123
0.0342
0.1212
-0.0601
-0.1176
-0.0029
-0.2419
0.282
0.1298
0.0677
-0.0222
-0.0135
0.0639
-0.0037
0.1288
18.9103
33.7981
-1.6608
7
28.6928
-9.9899
12.5036
3.6203
-4.029
6.2926
1.0407
2.5646
-0.4964
-0.5896
-0.7995
0.224
-0.0369
1.2624
-0.2412
0.4366
-0.052
-0.1046
0.3508
0.0997
0.2937
12.6483
37.3583
-11.8836
8
2.5176
-1.0739
-1.4517
6.0851
0.5225
1.5355
0.0567
0.1313
0.1127
-0.1575
0.0059
0.1195
-0.2122
0.1147
-0.0626
0.1096
-0.0225
-0.0021
0.0719
0.0046
0.1318
14.5083
33.1279
-6.6387
9
3.617
2.9895
1.5717
3.6873
-0.2328
2.6142
0.116
-0.0446
-0.1622
0.0038
-0.0243
-0.1246
0.156
-0.0395
-0.0917
0.0826
0.0137
-0.0031
0.0714
0.0063
0.1233
15.0422
13.8747
-3.4384
10
5.1972
0.5296
-2.8786
14.446
-11.1195
9.7457
0.2513
-0.2401
-0.1497
-0.1681
-0.4743
-0.1516
0.0082
0.4912
0.2231
0.098
-0.0064
0.0025
0.1201
-0.0006
0.1784
19.1206
14.9828
-5.0685
11
13.1541
-6.1815
-1.2276
7.6745
-0.8082
4.3643
0.0492
-0.0358
0.2954
0.0289
0.1062
0.0515
-0.2256
-0.0511
-0.1554
0.0767
-0.0081
-0.0039
0.0527
0.0089
0.107
11.3291
30.2619
-6.7612
12
6.7754
4.58
-2.2044
8.9135
-2.5709
7.1055
-0.1676
0.5293
0.5976
0.0226
0.4736
0.48
0.0576
-0.8352
-0.3061
0.0293
0.0225
-0.0194
0.2064
0.0477
0.1646
2.1412
27.6318
-6.7406
13
5.3955
-0.9977
-4.733
1.0275
2.7705
8.4178
0.0607
0.011
-0.0288
-0.0519
0.0409
-0.0553
-0.1315
0.0655
-0.1016
0.0974
-0.0119
-0.0026
0.0714
-0.0049
0.0951
11.8334
21.0699
-13.2107
14
5.8294
3.0717
0.0963
4.0671
1.1183
2.1601
0.0421
0.0904
-0.1563
-0.0706
0.0974
-0.1509
0.1525
0.2282
-0.1394
0.0797
0.027
0.001
0.0818
-0.0433
0.0779
13.5137
12.155
-17.829
15
9.0485
-0.6696
-0.4069
1.9717
-2.3956
4.3088
0.078
-0.1588
-0.2913
-0.046
-0.1365
-0.0573
0.242
0.3997
0.0585
0.0972
0.0181
-0.0056
0.0859
-0.0151
0.0977
12.0279
7.6057
-12.2614
16
8.0937
-6.1604
-4.2993
7.1959
6.3137
6.877
0.0463
-0.0145
-0.2044
0.0111
-0.0988
-0.0163
0.0213
-0.4586
0.0525
0.1019
-0.0271
0.0086
0.1599
-0.0092
0.1203
-3.368
12.8936
-7.9429
17
2.1751
-1.1809
0.572
2.0352
2.747
6.8607
0.1134
0.0277
0.2204
-0.4703
0.3489
-0.3545
-0.8433
0.7954
-0.4622
0.2337
-0.146
0.0772
0.225
-0.038
0.1021
14.4707
26.0483
-23.1046
18
6.6346
0.0792
3.8114
2.7043
-0.5033
6.0976
-0.0664
0.637
-0.0736
-0.254
0.1962
0.1222
-0.1558
0.2226
-0.1298
0.1493
-0.0185
0.005
0.2219
-0.0198
0.0126
5.061
17.0465
-41.3824
19
0.3658
0.4883
-0.5889
1.6792
-2.5681
16.0231
0.0341
0.1706
0.0332
-0.1946
0.0441
0.1162
-0.0597
0.1462
-0.0782
0.1424
0.0102
-0.0029
0.1425
-0.0045
0.0568
6.3716
20.6555
-29.6041
20
6.6845
-1.8549
9.4089
6.5872
1.9844
17.1107
-0.031
-0.6517
-0.0014
-0.0114
-0.1017
0.3193
0.0338
-1.3092
0.1327
0.0932
0.007
-0.0077
0.2219
0.0136
0.0795
-3.4407
19.6184
-23.9741
21
1.7108
-1.4096
3.2211
7.3592
-4.1728
13.6623
0.0136
0.1622
0.0709
-0.1236
0.2338
0.2602
-0.2585
-0.2737
-0.2474
0.1433
0.0117
-0.037
0.1875
0.0709
0.0524
-3.1117
25.7064
-38.2053
22
14.5995
2.7544
-3.5382
4.2277
-2.575
6.1945
0.1098
0.6374
-0.1549
-0.5448
0.1549
0.2844
0.0543
-0.2282
-0.2647
0.2061
0.0138
-0.0821
0.2247
0.0458
0.0612
-7.2826
20.8336
-42.7941
23
31.139
8.9039
-11.2961
18.6867
5.4098
28.9793
-0.0318
-1.0827
0.4878
0.8943
-0.108
2.1474
1.5892
0.0876
0.1398
0.2233
0.1635
0.064
0.4424
0.0827
0.3236
-16.4484
23.3962
-33.1829
24
6.118
-2.1355
-2.539
8.506
3.1054
5.2936
-0.1431
0.175
0.0366
0.0923
0.2535
0.5533
-0.0381
-0.1294
-0.1104
0.1133
0.0387
-0.0459
0.245
0.075
0.1063
-10.2109
20.1815
-34.1389
25
8.2634
1.4269
1.8579
2.7552
1.3891
5.8316
0.0882
0.394
-0.5654
-0.1982
0.1528
0.2803
0.3761
0.0366
-0.241
0.185
-0.0167
-0.0353
0.2182
-0.0744
0.1379
4.5773
9.8518
-38.3949
26
2.9094
-3.446
-2.0816
7.7147
0.9247
2.2665
-0.224
0.2595
-0.106
0.2982
0.3002
0.3708
0.0676
-0.3309
-0.0762
0.153
-0.0511
-0.0505
0.2428
-0.0313
0.1135
-3.9211
15.5529
-34.7717
27
35.9714
-3.3459
-13.288
3.9544
3.0239
5.7879
1.4569
-0.4674
3.5114
-0.5576
-0.1035
-0.7166
-0.7403
0.0496
-1.3534
0.7357
-0.1191
-0.1258
0.286
0.0889
0.5367
0.5001
29.3817
-33.4589
28
4.379
3.8495
-6.3977
11.3078
-14.194
18.618
0.0343
0.0938
0.0109
0.031
0.1836
0.2063
-0.0625
-0.2376
-0.2179
0.1312
0.0168
-0.0286
0.1535
-0.0044
0.0508
1.4835
19.192
-28.8427
29
7.1218
1.6442
-1.1311
11.6991
2.587
9.3506
0.1033
-0.0457
-0.3014
-0.5091
0.032
0.4709
0.2632
-0.5446
-0.1353
0.0944
-0.0304
-0.0429
0.1659
0.0041
0.0811
-1.616
11.2668
-25.5473
30
11.2998
0.7965
1.573
1.7417
-0.027
3.0463
0.0487
0.152
-0.4293
-0.1679
0.0346
-0.13
0.2942
0.1509
-0.0833
0.1001
0.0285
0.0047
0.0848
-0.0427
0.0459
10.8817
9.2983
-24.7758
31
4.8897
6.0264
-1.1808
11.1953
-0.8412
5.085
-0.0834
0.4619
-0.3456
-0.2208
0.1341
-0.2719
0.434
0.1388
-0.0507
0.1408
0.0382
-0.0002
0.1457
-0.0748
0.0724
11.0382
8.9537
-30.7572
32
39.5368
-7.7292
13.1456
19.8772
-13.0854
18.8177
-0.041
0.2418
1.3168
0.1762
0.1512
-0.0241
-0.8535
-0.2222
-0.1101
0.1852
-0.0591
0.0896
0.3097
-0.0024
0.0909
16.5059
24.5988
-33.3773
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
241 - 247
2
X-RAY DIFFRACTION
2
A
248 - 254
3
X-RAY DIFFRACTION
3
A
255 - 261
4
X-RAY DIFFRACTION
4
A
262 - 267
5
X-RAY DIFFRACTION
5
A
268 - 278
6
X-RAY DIFFRACTION
6
A
279 - 285
7
X-RAY DIFFRACTION
7
A
286 - 292
8
X-RAY DIFFRACTION
8
A
296 - 304
9
X-RAY DIFFRACTION
9
A
305 - 311
10
X-RAY DIFFRACTION
10
A
312 - 316
11
X-RAY DIFFRACTION
11
A
317 - 322
12
X-RAY DIFFRACTION
12
A
323 - 327
13
X-RAY DIFFRACTION
13
A
328 - 335
14
X-RAY DIFFRACTION
14
A
336 - 347
15
X-RAY DIFFRACTION
15
A
348 - 360
16
X-RAY DIFFRACTION
16
A
361 - 367
17
X-RAY DIFFRACTION
17
B
221 - 245
18
X-RAY DIFFRACTION
18
B
246 - 254
19
X-RAY DIFFRACTION
19
B
255 - 261
20
X-RAY DIFFRACTION
20
B
262 - 266
21
X-RAY DIFFRACTION
21
B
267 - 274
22
X-RAY DIFFRACTION
22
B
275 - 283
23
X-RAY DIFFRACTION
23
B
284 - 288
24
X-RAY DIFFRACTION
24
B
297 - 305
25
X-RAY DIFFRACTION
25
B
306 - 312
26
X-RAY DIFFRACTION
26
B
313 - 321
27
X-RAY DIFFRACTION
27
B
322 - 327
28
X-RAY DIFFRACTION
28
B
328 - 332
29
X-RAY DIFFRACTION
29
B
333 - 337
30
X-RAY DIFFRACTION
30
B
338 - 348
31
X-RAY DIFFRACTION
31
B
349 - 361
32
X-RAY DIFFRACTION
32
B
362 - 367
+
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