- PDB-3zs8: S. cerevisiae Get3 complexed with a cytosolic Get1 fragment -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3zs8
Title
S. cerevisiae Get3 complexed with a cytosolic Get1 fragment
Components
ATPASE GET3
GOLGI TO ER TRAFFIC PROTEIN 1
Keywords
HYDROLASE/TRANSPORT PROTEIN / HYDROLASE-TRANSPORT PROTEIN COMPLEX / MEMBRANE PROTEIN / TARGETING FACTOR
Function / homology
Function and homology information
GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to metal ion / mitophagy ...GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to metal ion / mitophagy / protein-membrane adaptor activity / protein folding chaperone / guanyl-nucleotide exchange factor activity / mitochondrial membrane / unfolded protein binding / response to heat / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol Similarity search - Function
Resolution: 3→47.215 Å / SU ML: 0.97 / σ(F): 1.34 / Phase error: 28.18 / Stereochemistry target values: ML Details: ELECTRON DENSITY IS WEAKEST IN THE HELICAL SUBDOMAINS. DISORDERED SIDECHAINS WERE MODELED STEREOCHEMICALLY
Rfactor
Num. reflection
% reflection
Rfree
0.2807
2334
10 %
Rwork
0.2202
-
-
obs
0.2261
23431
98.85 %
Solvent computation
Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.117 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
14.4602 Å2
0 Å2
0 Å2
2-
-
14.4602 Å2
0 Å2
3-
-
-
-28.9205 Å2
Refinement step
Cycle: LAST / Resolution: 3→47.215 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5644
0
1
0
5645
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.004
5736
X-RAY DIFFRACTION
f_angle_d
0.83
7719
X-RAY DIFFRACTION
f_dihedral_angle_d
14.663
2165
X-RAY DIFFRACTION
f_chiral_restr
0.062
873
X-RAY DIFFRACTION
f_plane_restr
0.003
988
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Number
Refine-ID
Type
Rms dev position (Å)
1
1
A
1853
X-RAY DIFFRACTION
POSITIONAL
1
2
B
1853
X-RAY DIFFRACTION
POSITIONAL
0.02
2
1
C
306
X-RAY DIFFRACTION
POSITIONAL
2
2
D
306
X-RAY DIFFRACTION
POSITIONAL
0.016
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3.0001-3.0613
0.4035
115
0.3306
1094
X-RAY DIFFRACTION
88
3.0613-3.1279
0.3645
124
0.2849
1167
X-RAY DIFFRACTION
96
3.1279-3.2006
0.3165
137
0.2685
1206
X-RAY DIFFRACTION
100
3.2006-3.2807
0.3197
149
0.2364
1216
X-RAY DIFFRACTION
100
3.2807-3.3693
0.2925
128
0.2367
1227
X-RAY DIFFRACTION
100
3.3693-3.4685
0.2921
134
0.2175
1235
X-RAY DIFFRACTION
100
3.4685-3.5804
0.2828
138
0.2179
1222
X-RAY DIFFRACTION
100
3.5804-3.7083
0.262
132
0.213
1249
X-RAY DIFFRACTION
100
3.7083-3.8567
0.3197
138
0.2151
1215
X-RAY DIFFRACTION
100
3.8567-4.0321
0.2786
142
0.2129
1241
X-RAY DIFFRACTION
100
4.0321-4.2446
0.2544
135
0.1991
1266
X-RAY DIFFRACTION
100
4.2446-4.5103
0.2701
141
0.1811
1232
X-RAY DIFFRACTION
100
4.5103-4.8582
0.2031
137
0.1575
1261
X-RAY DIFFRACTION
100
4.8582-5.3465
0.2508
144
0.1954
1263
X-RAY DIFFRACTION
100
5.3465-6.1188
0.3471
142
0.2628
1296
X-RAY DIFFRACTION
100
6.1188-7.7036
0.3352
144
0.2552
1301
X-RAY DIFFRACTION
100
7.7036-47.2206
0.2571
154
0.2291
1406
X-RAY DIFFRACTION
98
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
1.0401
0.458
-1.4241
0.3017
-0.5118
0.8972
0.0364
-0.252
-0.059
0.2599
-0.2817
0.1087
0.3554
0.0818
-0.0074
0.3744
-0.0475
-0.0017
0.9127
0.0634
0.5263
32.9905
-55.1043
16.5555
2
-0.0906
-0.123
-0.0038
0.277
0.1201
0.0465
-0.0876
0.2302
-0.0174
0.1257
0.5317
-0.1306
-0.4213
0.1822
0.0001
0.7579
0.1381
-0.1007
0.8762
-0.2575
0.944
24.2474
-27.8574
35.2644
3
0.994
-0.3146
0.6904
0.2865
0.9079
0.2854
-0.098
-0.19
-0.0573
0.058
0.0037
0.0431
-0.1681
0.0762
-0.0874
0.263
-0.0116
-0.0264
0.6794
-0.0116
0.4996
0.4544
-35.4861
14.6992
4
-0.1407
0.0779
-0.1287
0.3873
-0.2849
0.0858
0.2586
0.031
0.3007
0.4764
0.0556
-0.6612
0.1493
-0.2014
-0.0001
0.6721
-0.0378
-0.0171
0.6726
0.1417
0.6163
8.1647
-58.4381
37.5428
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINAANDRESID1:354
2
X-RAY DIFFRACTION
2
CHAINCANDRESID521:604
3
X-RAY DIFFRACTION
3
CHAINBANDRESID1:354
4
X-RAY DIFFRACTION
4
CHAINDANDRESID521:604
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