- PDB-3ibg: Crystal structure of Aspergillus fumigatus Get3 with bound ADP -
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Basic information
Entry
Database: PDB / ID: 3ibg
Title
Crystal structure of Aspergillus fumigatus Get3 with bound ADP
Components
ATPase, subunit of the Get complex
Keywords
HYDROLASE / nucleotide binding / deviant Walker A motif
Function / homology
Function and homology information
GET complex / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding Similarity search - Function
A: ATPase, subunit of the Get complex B: ATPase, subunit of the Get complex C: ATPase, subunit of the Get complex D: ATPase, subunit of the Get complex E: ATPase, subunit of the Get complex F: ATPase, subunit of the Get complex hetero molecules
Method: X-RAY DIFFRACTION / Number of used crystals: 2
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Sample preparation
Crystal
Density Matthews: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M potassium citrate, 16% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING 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
SSRL
BL12-2
1
1
SYNCHROTRON
SSRL
BL12-2
2
0.97941, 0.97954, 0.91837
Detector
Type
ID
Detector
Date
MARMOSAIC 325 mm CCD
1
CCD
Dec 14, 2008
MARMOSAIC 325 mm CCD
2
CCD
Jan 12, 2009
Radiation
ID
Monochromator
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
LIQUIDN2COOLEDDOUBLECRYSTAL
SINGLEWAVELENGTH
M
x-ray
1
2
LIQUIDN2COOLEDDOUBLECRYSTAL
MAD
M
x-ray
1
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1
1
2
0.97941
1
3
0.97954
1
4
0.91837
1
Reflection
Redundancy: 7.3 % / Av σ(I) over netI: 7.2 / Number: 118718 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / D res high: 4.499 Å / D res low: 80.927 Å / Num. obs: 16179 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Rsym value
Redundancy
14.23
80.93
99.6
1
0.041
0.041
6
10.06
14.23
100
1
0.045
0.045
6.9
8.22
10.06
100
1
0.052
0.052
7.1
7.12
8.22
100
1
0.067
0.067
7.3
6.36
7.12
100
1
0.106
0.106
7.4
5.81
6.36
100
1
0.111
0.111
7.4
5.38
5.81
100
1
0.107
0.107
7.4
5.03
5.38
100
1
0.101
0.101
7.5
4.74
5.03
100
1
0.104
0.104
7.5
4.5
4.74
100
1
0.12
0.12
7.5
Reflection
Resolution: 3.2→65.268 Å / Num. obs: 43190 / % possible obs: 100 % / Redundancy: 4.9 % / Rsym value: 0.124 / Net I/σ(I): 10.4
Reflection shell
Resolution: 3.2→3.37 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.667 / % possible all: 100
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Phasing
Phasing
Method: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-ID
Expt-ID
Set-ID
Wavelength (Å)
F double prime refined
F prime refined
3wavelength
1
1
0.979
3.7
-10.7
3wavelength
1
2
0.918
3.4
-1.8
3wavelength
1
3
0.979
5.7
-8.8
Phasing MAD set site
ID
Atom type symbol
B iso
Fract x
Fract y
Fract z
Occupancy
1
Se
60
0.964
0.317
0.788
1.667
2
Se
60
0.199
0.171
0.958
1.858
3
Se
60
0.435
0.145
0.931
1.252
4
Se
60
0.21
0.311
0.764
2.484
5
Se
60
0.063
0.579
0.9
1.569
6
Se
60
0.865
0.5
0.732
2.104
7
Se
60
0.087
0.506
0.695
1.859
8
Se
60
0.199
0.341
0.935
0.937
9
Se
60
0.307
0.422
0.781
1.074
10
Se
60
0.355
0.728
0.837
1.504
11
Se
39.762
0.996
0.845
0.933
0.891
12
Se
60
0.277
0.454
0.991
1.436
13
Se
60
0.377
0.972
0.914
1.463
14
Se
60
0.469
0.863
0.969
1.172
15
Se
60
0.233
0.432
0.979
1.653
16
Se
60
0.728
0.954
0.885
1.415
17
Se
60
0.01
0.451
0.026
1.375
18
Se
60
1
0.293
0.992
1.319
19
Se
60
0.618
0.285
0.767
0.983
20
Se
60
0.951
0.476
0.804
1.349
21
Se
60
0.551
0.361
0.778
1.191
22
Se
60
0.771
0.233
0.995
1.503
23
Se
60
0.713
0.527
0.822
1.253
24
Se
57.171
0.198
0.84
0.914
0.738
25
Se
60
0.503
0.47
0.867
1.605
26
Se
60
0.333
0.475
0.897
1.266
27
Se
60
0.372
0.736
0.859
1.003
28
Se
60
0.202
0.706
0.784
1.286
29
Se
60
0.659
0.024
0.908
1.263
30
Se
60
0.01
0.588
0.884
1.665
31
Se
60
0.105
0.394
0.665
1.217
32
Se
60
0.012
0.812
0.936
1.08
33
Se
60
0.815
0.339
0.727
1.558
34
Se
60
0.847
0.921
0.964
0.979
35
Se
60
0.58
0.897
0.89
1.641
36
Se
60
0.505
0.503
0.873
1.436
37
Se
60
0.999
0.412
0.964
1.314
38
Se
60
0.038
0.947
0.902
1.066
39
Se
42.086
0.465
0.885
0.951
1.021
40
Se
60
0.786
0.623
0.874
1.427
41
Se
60
0.472
0.687
0.786
0.928
42
Se
60
0.265
0.889
0.969
1.123
43
Se
60
0.419
0.433
0.949
0.92
44
Se
60
0.678
0.391
0.856
1.133
45
Se
60
0.162
0.707
0.868
1.867
46
Se
60
0.958
0.613
0.813
1.429
47
Se
60
0.206
0.61
0.858
0.955
48
Se
1
0.038
0.511
0.712
0.112
49
Se
1
0.662
0.538
0.74
0.012
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Processing
Software
Name
Version
Classification
NB
SCALA
3.3.9
dataprocessing
SOLVE
2.13
phasing
PHENIX
1.4_62
refinement
PDB_EXTRACT
3.005
dataextraction
Blu-Ice
datacollection
MOSFLM
datareduction
SCALA
datascaling
Refinement
Method to determine structure: MAD / Resolution: 3.2→65.264 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 1.35 / Phase error: 24.1 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2513
2197
5.1 %
Rwork
0.2119
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obs
0.2139
43100
99.92 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.369 Å2 / ksol: 0.332 e/Å3