E3ubiquitin-proteinligaseUHRF1 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / Ubiquitin-like-containing PHD and ...Ubiquitin-like PHD and RING finger domain-containing protein 1 / Ubiquitin-like-containing PHD and RING finger domains protein 1 / Inverted CCAAT box-binding protein of 90 kDa / Transcription factor ICBP90 / Nuclear zinc finger protein Np95 / Nuclear protein 95 / HuNp95 / RING finger protein 106
Mass: 23910.240 Da / Num. of mol.: 1 / Fragment: SRA Domain: Residues 414-617 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Plasmid: pNIC-CH / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q96T88, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1:1 ratio of protein (34 mg/ml) solution and well solution consisting of 1.4 M Ammonium sulfate, 0.1 M Bis-Tris pH 6.0, 0.2 M NaCl, 1 mM TCEP. Crystals cryoprotected by immersion in the well ...Details: 1:1 ratio of protein (34 mg/ml) solution and well solution consisting of 1.4 M Ammonium sulfate, 0.1 M Bis-Tris pH 6.0, 0.2 M NaCl, 1 mM TCEP. Crystals cryoprotected by immersion in the well solution mixed in 1:1 ratio with a water solution containing 20% (w/v) Sucrose, 4% (w/v) Glucose, 18% (v/v) Glycerol and 18% (v/v) Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution: 1.7→1.76 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 2670 / Rsym value: 0.9 / % possible all: 100
-
Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
HKL-2000
datacollection
HKL-2000
datareduction
HKL-2000
datascaling
SOLVE
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.7→32.99 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.287 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19658
1369
5.1 %
RANDOM
Rwork
0.15851
-
-
-
obs
0.16043
25677
99.39 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 15.105 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.77 Å2
0.38 Å2
0 Å2
2-
-
0.77 Å2
0 Å2
3-
-
-
-1.15 Å2
Refinement step
Cycle: LAST / Resolution: 1.7→32.99 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1547
0
28
210
1785
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.021
1616
X-RAY DIFFRACTION
r_angle_refined_deg
1.519
1.942
2190
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.149
5
201
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.958
23.165
79
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.326
15
238
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.645
15
13
X-RAY DIFFRACTION
r_chiral_restr
0.121
0.2
216
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
1280
X-RAY DIFFRACTION
r_nbd_refined
0.199
0.2
724
X-RAY DIFFRACTION
r_nbtor_refined
0.309
0.2
1100
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.131
0.2
153
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.261
0.2
51
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.119
0.2
20
X-RAY DIFFRACTION
r_mcbond_it
1.055
1.5
1005
X-RAY DIFFRACTION
r_mcangle_it
1.471
2
1573
X-RAY DIFFRACTION
r_scbond_it
2.207
3
707
X-RAY DIFFRACTION
r_scangle_it
3.265
4.5
617
LS refinement shell
Resolution: 1.7→1.744 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.284
93
-
Rwork
0.207
1868
-
obs
-
-
98.49 %
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
2.2406
-2.1607
0.3584
10.1697
0.7156
2.8855
-0.0031
-0.0592
0.2333
0.3106
-0.0496
-0.5498
-0.2141
0.4909
0.0526
0.001
-0.0627
-0.0245
0.0891
0.0056
0.0526
9.4852
45.7618
10.7113
2
2.0689
0.3008
-1.4843
1.4434
-2.0305
3.4175
-0.0422
0.0097
-0.0577
0.068
-0.0718
0.0416
0.2459
0.0463
0.1139
0.0479
-0.0151
-0.0036
0.0661
0.0086
0.0453
1.7839
33.4669
14.8822
3
8.2507
0.465
-1.7516
2.9351
-0.3725
7.2564
0.0964
-0.0595
-0.2632
0.0348
-0.1539
-0.0861
-0.2803
0.3464
0.0574
0.0386
-0.0437
-0.0173
0.0868
0.015
0.049
4.4086
41.5176
17.182
4
3.2782
0.5194
-1.3974
2.9515
-1.7204
1.3788
-0.012
-0.3368
0.0333
0.3188
-0.1486
-0.2359
-0.4242
0.058
0.1606
0.1367
-0.0595
-0.0277
0.0563
-0.025
0.0226
-0.0159
50.9694
15.9232
5
10.0476
3.593
0.6337
8.4827
-1.6069
1.9622
0.085
-0.4076
0.5154
0.2441
-0.0181
0.9801
-0.1111
-0.4044
-0.0669
0.0044
-0.011
0.0412
0.057
-0.0289
0.0921
-9.626
42.8774
11.2704
6
4.3203
0.1959
-0.6498
7.7046
1.7146
7.6669
0.0576
-0.0671
0.1792
0.1872
-0.1504
0.6005
-0.07
-0.3815
0.0928
0.0415
-0.0324
0.0238
0.0472
-0.0039
0.0975
-12.3484
42.8916
2.9448
7
12.2228
2.8161
3.3023
8.1984
-0.5426
3.1302
-0.0663
-0.8201
0.701
0.6793
-0.0718
0.6893
-0.1747
-0.4112
0.1381
0.1156
-0.0013
0.1286
0.021
-0.0619
0.0346
-12.8714
56.8422
15.2162
8
0.8008
0.586
-1.8185
2.7181
-2.5046
5.6778
0.0731
-0.061
0.1823
0.1345
0.0026
0.0989
-0.2544
0.036
-0.0757
0.0864
-0.0446
0.0017
0.0056
-0.0093
0.0697
-3.1536
57.8079
6.2185
9
7.1148
-1.0117
-4.4875
6.7731
5.4528
13.3377
0.2107
0.2434
0.3348
-0.1681
-0.3341
0.5929
-0.7616
-0.4788
0.1234
0.1304
-0.006
0.0043
0.0008
0.0296
0.1468
-9.4048
61.8126
1.7452
10
1.0431
1.0795
-0.4613
2.48
-0.672
1.4986
0.012
-0.0416
0.0401
-0.0006
-0.0084
0.0824
-0.0216
-0.0837
-0.0036
0.0813
-0.0274
0.0051
0.0783
-0.0051
0.0951
-4.5773
42.8818
5.7116
11
3.2435
1.0152
2.6491
6.2048
-2.1001
9.3239
0.0738
-0.0116
0.0897
-0.0485
-0.0675
0.0768
0.2133
-0.172
-0.0063
0.0804
-0.0419
-0.0076
0.042
-0.0147
0.0648
-9.8405
31.9166
5.9904
12
0.5961
-0.7736
0.5027
1.0099
-0.7428
1.8198
0.0293
-0.0441
0.0915
0.0031
-0.0932
-0.018
0.0117
0.0747
0.0639
0.0666
-0.037
0.0002
0.0475
0.0057
0.0715
-1.0509
41.356
4.764
13
11.3456
-0.2768
-0.2986
6.5559
-3.3937
2.401
-0.138
0.5132
0.1901
-0.0449
0.1884
0.4549
-0.0881
-0.3149
-0.0503
0.0476
-0.0149
0.0171
0.0197
-0.0019
0.0995
-12.6964
55.949
2.8098
14
18.6732
6.7978
-16.2077
11.6614
-11.0161
62.901
0.0824
-0.1676
0.3352
1.0866
-0.1635
0.9289
1.1327
-2.8535
0.0811
0.0765
-0.1482
0.2034
0.1395
-0.0653
0.2135
-23.7186
53.1726
11.5054
15
4.4907
-3.9983
-4.3882
4.5926
1.5072
9.8643
-0.1756
0.4196
-0.0512
0.4164
-0.0664
0.5144
0.1948
-0.4941
0.242
0.0612
-0.0363
0.073
0.0214
-0.0259
0.1118
-14.6336
54.3175
8.2943
16
2.1781
-2.0877
-0.4289
3.9329
0.4908
1.0024
0.0319
0.081
0.021
-0.1494
-0.094
-0.0947
0.0742
0.1348
0.0621
0.0746
-0.0241
0.0081
0.0694
-0.0028
0.0504
0.0065
38.398
-2.4431
17
9.507
-3.6229
-0.6965
14.9198
1.8685
15.6251
-0.0456
0.2397
0.1956
-0.3541
-0.0312
-0.2211
0.8301
0.0714
0.0768
0.0545
0.055
0.0152
0.016
0.0012
0.0377
5.3699
27.1426
-0.7493
18
11.8915
2.2628
-12.1812
5.0766
-2.8962
29.5856
-0.3244
-0.1798
-0.171
0.0873
-0.0454
-0.1987
1.0483
1.0795
0.3698
0.0919
0.0634
-0.0345
0.0165
0.0121
0.0141
7.2667
25.929
6.9147
19
3.085
2.9869
-1.6464
9.8277
-7.7099
15.8452
0.0424
-0.0095
-0.2726
-0.2922
-0.2522
-0.1086
0.8364
0.7077
0.2098
0.07
0.0687
0.0071
0.0543
0.0165
0.0452
3.4194
23.315
22.4749
20
24.6922
22.4887
-19.1661
24.5428
-7.1315
41.1245
-0.6053
-0.0536
-0.6604
-0.4796
-0.5682
-0.2819
1.934
-0.5407
1.1735
0.1605
0.02
0.0452
-0.0573
0.0123
0.0525
-2.7276
16.5213
28.3319
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
414 - 424
2 - 12
2
X-RAY DIFFRACTION
2
A
A
425 - 437
13 - 25
3
X-RAY DIFFRACTION
3
A
A
438 - 444
26 - 32
4
X-RAY DIFFRACTION
4
A
A
445 - 458
33 - 46
5
X-RAY DIFFRACTION
5
A
A
459 - 466
47 - 54
6
X-RAY DIFFRACTION
6
A
A
467 - 478
55 - 66
7
X-RAY DIFFRACTION
7
A
A
479 - 504
67 - 92
8
X-RAY DIFFRACTION
8
A
A
505 - 515
93 - 103
9
X-RAY DIFFRACTION
9
A
A
516 - 525
104 - 113
10
X-RAY DIFFRACTION
10
A
A
526 - 543
114 - 131
11
X-RAY DIFFRACTION
11
A
A
544 - 551
132 - 139
12
X-RAY DIFFRACTION
12
A
A
552 - 562
140 - 150
13
X-RAY DIFFRACTION
13
A
A
563 - 566
151 - 154
14
X-RAY DIFFRACTION
14
A
A
567 - 573
155 - 161
15
X-RAY DIFFRACTION
15
A
A
574 - 578
162 - 166
16
X-RAY DIFFRACTION
16
A
A
579 - 593
167 - 181
17
X-RAY DIFFRACTION
17
A
A
594 - 599
182 - 187
18
X-RAY DIFFRACTION
18
A
A
600 - 605
188 - 193
19
X-RAY DIFFRACTION
19
A
A
606 - 613
194 - 201
20
X-RAY DIFFRACTION
20
A
A
614 - 619
202 - 207
+
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