negative regulation of sodium ion transmembrane transporter activity / HECT-type E3 ubiquitin transferase / regulation of dendrite morphogenesis / Degradation of DVL / negative regulation of canonical Wnt signaling pathway / protein polyubiquitination / positive regulation of protein catabolic process / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process ...negative regulation of sodium ion transmembrane transporter activity / HECT-type E3 ubiquitin transferase / regulation of dendrite morphogenesis / Degradation of DVL / negative regulation of canonical Wnt signaling pathway / protein polyubiquitination / positive regulation of protein catabolic process / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / cytoplasm / cytosol Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE COMPLETE SEQUENCE USED FOR CRYSTALLIZATION IS: ...THE COMPLETE SEQUENCE USED FOR CRYSTALLIZATION IS: GSEAESSQSSLDLRREGSLSPVNSQKITLLLQSPAVKFITNPEFFTVLHAN YSAYRVFTSSTCLKHMILKVRRDARNFERYQHNRDLVNFINMFADTRLELP RGWEIKTDQQGKSFFVDHNSRATTFIDPRIPLQNG. THE PROTEIN WAS CRYSTALLIZED IN THE PRESENCE OF TRYPSIN AND THE ACTUAL CRYSTALLIZED PROTEIN SEQUENCE MAY BE SHORTER. ONLY THE ORDERED PART OF THE PROTEIN IS REPORTED IN SEQRES RECORDS.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 1.75 Å3/Da / Density % sol: 29.83 %
Crystal grow
Temperature: 291.1 K / Method: vapor diffusion, sitting drop / pH: 8 Details: equal volumes of protein (10 mg/ml) [containing 0.1 MM actetic acid PH 3.0] was mixed with crystallization buffer (1.0 M sodium citrate, 0.1 MM immidazole PH 8.0), along with trypsin at a ...Details: equal volumes of protein (10 mg/ml) [containing 0.1 MM actetic acid PH 3.0] was mixed with crystallization buffer (1.0 M sodium citrate, 0.1 MM immidazole PH 8.0), along with trypsin at a concentration of 1 mg trypsin/500 mg protein. cryoprotected with 15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 291.1K
Resolution: 1.8→1.83 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 5.462 / Num. unique all: 412 / Rsym value: 0.256 / % possible all: 99.8
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Processing
Software
Name
Version
Classification
HKL-3000
datacollection
SOLVE
phasing
REFMAC
5.5.0102
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 1.8→29.45 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.608 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.13 / 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
0.19956
413
4.9 %
RANDOM
Rwork
0.14995
-
-
-
obs
0.15228
7986
99.79 %
-
all
-
8513
-
-
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: 24.812 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.02 Å2
0 Å2
-0.01 Å2
2-
-
-0.02 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→29.45 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
902
0
4
72
978
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
960
X-RAY DIFFRACTION
r_angle_refined_deg
1.546
1.936
1303
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.205
5
115
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.195
22.653
49
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.804
15
163
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.024
15
9
X-RAY DIFFRACTION
r_chiral_restr
0.106
0.2
142
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.021
749
X-RAY DIFFRACTION
r_mcbond_it
0.738
1.5
573
X-RAY DIFFRACTION
r_mcangle_it
1.263
2
935
X-RAY DIFFRACTION
r_scbond_it
2.35
3
387
X-RAY DIFFRACTION
r_scangle_it
3.64
4.5
368
LS refinement shell
Resolution: 1.8→1.847 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.233
30
-
Rwork
0.149
589
-
obs
-
-
100 %
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
9.736
8.868
-0.2207
15.8897
-2.8551
6.4823
-0.6136
0.9708
0.2713
-0.501
0.3734
-0.0326
-0.1928
0.6034
0.2402
0.1798
-0.0895
-0.001
0.2364
0.0663
0.0795
4.7546
37.1568
24.7555
2
3.8792
0.1214
-0.7455
2.6155
-0.5598
2.547
-0.0246
-0.0118
0.0926
0.0008
0.0169
0.0177
-0.0728
-0.0817
0.0077
0.04
-0.0056
-0.0024
0.0594
-0.0083
0.06
-3.4466
35.164
34.9054
3
4.8463
-3.0552
1.3549
12.2587
-5.4716
1.3046
-0.0369
-0.0753
0.1091
0.328
0.1825
0.2135
-0.1703
-0.0699
-0.1455
0.0818
-0.003
0.0201
0.0878
0.0166
0.0776
-5.9128
25.3389
42.6929
4
1.8963
1.8583
-0.347
2.1659
-3.6249
3.5427
0.1464
-0.3327
0.0441
0.3397
-0.2879
-0.1317
-0.0742
0.3301
0.1415
0.1995
-0.0052
-0.0208
0.2045
0.014
0.1769
1.0362
25.661
45.8829
5
0.966
3.784
-0.9753
11.4177
-1.7255
11.7817
0.1151
-0.4125
-0.0293
0.1568
-0.0103
-0.3936
0.3697
0.3607
-0.1047
0.0608
-0.0073
-0.0259
0.1703
-0.0144
0.0679
7.8549
31.9892
42.3917
6
9.6186
0.3672
-2.2822
7.1219
1.3837
4.5902
0.0902
-0.355
0.6061
0.3315
-0.0638
-0.2816
-0.0908
0.4036
-0.0264
0.0461
-0.012
-0.0063
0.0699
-0.0208
0.0896
6.7378
39.9138
37.7875
7
13.9809
-5.5865
-5.2186
1.1671
1.4778
7.389
0.1404
0.2036
0.3769
-0.1146
0.0893
-0.1297
-0.4446
0.0186
-0.2298
0.0968
0.0062
0.0168
0.1189
0.0179
0.094
10.2101
37.6506
30.836
8
5.0247
2.5472
1.9635
8.3404
1.0694
2.9955
-0.1381
0.3261
-0.198
-0.5774
0.171
-0.2219
0.0226
0.099
-0.0329
0.0854
0.0001
0.0203
0.0919
-0.0072
0.0626
12.5187
30.9489
31.6424
9
20.9399
9.6864
-0.9724
10.8167
-0.0995
5.3584
0.1213
0.1191
-0.8877
0.2915
-0.0753
-0.5083
0.4066
0.133
-0.046
0.0973
0.0116
-0.0034
0.0432
-0.008
0.0648
8.2246
23.1084
34.5828
10
3.5722
-0.7293
-1.3249
0.3934
-1.4134
2.7998
0.0128
-0.1308
-0.1295
-0.0124
0.033
0.0819
-0.0997
-0.1088
-0.0458
0.1174
-0.0054
0.0176
0.0973
-0.0134
0.0841
-0.6459
24.6141
34.1363
11
16.2256
3.985
-5.8963
7.9297
-2.1023
7.8041
0.167
0.2638
-0.2971
-0.2858
0.1566
0.3467
0.6597
-1.1905
-0.3236
0.1159
-0.0466
-0.0329
0.2443
-0.0564
0.1686
-9.1275
21.2339
24.1135
12
5.3316
1.5429
-1.9717
7.6042
0.7774
7.8195
0.1172
0.61
0.0696
-0.2934
0.0295
0.0648
-0.0706
-0.3595
-0.1467
0.0846
0.0345
-0.0137
0.1326
-0.0228
-0.0008
-0.386
24.4115
17.3068
13
10.3057
6.267
0.5297
21.678
-10.5488
15.655
-0.0033
-0.1674
-0.7251
-0.3052
0.0855
-0.1547
0.9706
0.4032
-0.0822
0.2862
0.1266
-0.0276
0.2374
-0.1044
0.2311
6.7192
16.27
21.1762
14
7.2074
3.0157
-1.0802
9.2656
-5.6055
14.958
0.0586
0.8114
0.5855
-0.2016
0.2238
0.5435
-0.6847
0.19
-0.2824
0.173
0.0109
0.041
0.1801
0.0191
0.0895
4.0745
27.121
16.9582
15
5.9702
2.7049
-8.2634
9.2634
-8.7437
30.3771
0.0261
0.3535
0.6156
-0.7289
-0.0841
-0.345
-0.4982
0.8946
0.058
0.1237
-0.0357
0.0199
0.1953
0.017
0.1509
7.5967
26.8909
22.1749
16
5.9083
-1.7245
-2.3331
2.3445
1.6826
2.9161
0.1033
0.282
0.0581
-0.0347
-0.0761
-0.0176
-0.0417
-0.141
-0.0273
0.0699
0.0067
-0.0111
0.0925
0.0042
0.0187
-4.811
30.204
26.927
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
948 - 953
2
X-RAY DIFFRACTION
2
A
954 - 966
3
X-RAY DIFFRACTION
3
A
967 - 973
4
X-RAY DIFFRACTION
4
A
974 - 980
5
X-RAY DIFFRACTION
5
A
981 - 988
6
X-RAY DIFFRACTION
6
A
989 - 993
7
X-RAY DIFFRACTION
7
A
994 - 998
8
X-RAY DIFFRACTION
8
A
999 - 1003
9
X-RAY DIFFRACTION
9
A
1004 - 1008
10
X-RAY DIFFRACTION
10
A
1009 - 1014
11
X-RAY DIFFRACTION
11
A
1015 - 1019
12
X-RAY DIFFRACTION
12
A
1020 - 1026
13
X-RAY DIFFRACTION
13
A
1027 - 1035
14
X-RAY DIFFRACTION
14
A
1036 - 1040
15
X-RAY DIFFRACTION
15
A
1041 - 1047
16
X-RAY DIFFRACTION
16
A
1048 - 1056
+
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