- PDB-1z3h: The exportin Cse1 in its cargo-free, cytoplasmic state -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1z3h
Title
The exportin Cse1 in its cargo-free, cytoplasmic state
Components
Importin alpha re-exporter
Keywords
PROTEIN TRANSPORT / Cse1 / Exportin / Nuclear transport / HEAT repeat
Function / homology
Function and homology information
nuclear export signal receptor activity / snRNA import into nucleus / protein export from nucleus / positive regulation of protein export from nucleus / small GTPase binding / protein import into nucleus / nuclear envelope / cell cycle / cell division / protein-containing complex / cytosol Similarity search - Function
Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 2
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Sample preparation
Crystal
Density Matthews: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 8000, MgCl2, glycerol, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
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Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
ESRF
ID14-4
1
0.93
SYNCHROTRON
SLS
X06SA
2
1.02
Detector
Type
ID
Detector
Date
ADSC QUANTUM 4
1
CCD
Mar 5, 2004
MARRESEARCH
2
CCD
Jun 13, 2003
Radiation
ID
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
Monochromator
1
SINGLEWAVELENGTH
M
x-ray
1
2
SINGLEWAVELENGTH
M
x-ray
1
SAGITALLYFOCUSEDSi(111)
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.93
1
2
1.02
1
Reflection
Redundancy: 13.2 % / Av σ(I) over netI: 3.7 / Number: 33873 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / D res high: 3.3 Å / D res low: 122.06 Å / % possible obs: 98.6
Resolution: 3.3→3.48 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 5.5 / Rsym value: 0.391 / % possible all: 98.5
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Phasing
Phasing
Method: SAD
Phasing MAD set site
ID
Cartn x (Å)
Cartn y (Å)
Cartn z (Å)
Atom type symbol
B iso
Occupancy
1
9.01
6.419
72.673
SE
134.44
2.69
2
37.747
-27.557
84.104
SE
60
1.5
3
14.785
2.021
59.577
SE
123.38
2.43
4
31.862
-31.25
104.424
SE
60
1.25
5
31.476
8.705
107.899
SE
122.15
2.05
6
33.21
21.147
109.723
SE
0
1.38
7
52.516
-34.296
87.75
SE
60
1.36
8
52.672
-31.854
81.356
SE
60
1.28
9
22.075
42.635
99.39
SE
150.14
2.34
10
25.476
45.515
103.488
SE
130.1
2.25
11
32.016
-33.408
97.368
SE
91.8
1.48
12
47.282
-28.512
102.069
SE
60
1.14
13
4.184
39.099
79.905
SE
60
1.05
14
11.546
4.96
54.791
SE
60
0.86
15
29.669
-6.331
83.453
SE
60
0.87
16
8.687
63.746
132.795
SE
179.78
2.31
17
3.181
47.579
95.944
SE
60
0.88
18
50.415
14.998
72.31
SE
0
2.07
19
25.788
-16.231
45.779
SE
60
0.79
20
15.705
2.143
73.261
SE
60
0.88
21
22.581
-18.276
41.234
SE
60
0.83
22
14.767
59.16
119.886
SE
172.5
2.39
23
11.89
62.832
115.168
SE
60
0.64
24
53.946
3.078
75.584
SE
60
0.91
25
55.071
-10.353
101.189
SE
60
0.87
26
4.616
-10.57
36.355
SE
60
0.73
27
6.879
-16.365
19.51
SE
60
0.77
28
14.829
58.19
133.185
SE
60
0.76
29
27.107
-27.574
78.775
SE
60
0.71
30
42.269
-28.345
92.997
SE
60
0.57
31
134.203
4.245
113.772
SE
60
0.59
32
23.698
26.102
14.558
SE
60
0.53
33
103.689
9.259
70.808
SE
60
0.4
34
64.247
25.241
59.929
SE
60
0.42
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Processing
Software
Name
Version
Classification
NB
SHARP
phasing
SOLOMON
phasing
CNS
refinement
PDB_EXTRACT
1.6
dataextraction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
Refinement
Method to determine structure: SAD / Resolution: 3.1→122 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Residue side chains that were not visible in the final 2Fo-Fc map have been placed in the model but the B factors for these atoms have been set above 200. The protein was treated with ...Details: Residue side chains that were not visible in the final 2Fo-Fc map have been placed in the model but the B factors for these atoms have been set above 200. The protein was treated with subtilisin during purification. This resulted in two fragments of 100 kDa and 10 kDa respectively that co-purify and are both present in the crystal
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.288
2096
5 %
RANDOM
Rwork
0.241
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-
-
all
0.287
33873
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-
obs
0.287
33834
99.6 %
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Solvent computation
Bsol: 30.849 Å2
Displacement parameters
Biso mean: 77.326 Å2
Baniso -1
Baniso -2
Baniso -3
1-
16.882 Å2
0 Å2
0 Å2
2-
-
-22.698 Å2
0 Å2
3-
-
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5.816 Å2
Refinement step
Cycle: LAST / Resolution: 3.1→122 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
14786
0
1
0
14787
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
c_bond_d
0.01
X-RAY DIFFRACTION
c_angle_deg
1.543
0
LS refinement shell
Resolution: 3.1→3.2 Å
Rfactor
Num. reflection
% reflection
Rfree
0.406
186
-
Rwork
0.377
-
-
obs
-
3737
100 %
Xplor file
Refine-ID
Serial no
Param file
X-RAY DIFFRACTION
1
CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION
2
CNS_TOPPAR:ion.param
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