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- PDB-8had: A novel dimer configuration of a diatom Get3 forming a tetrameric... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8had | ||||||
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Title | A novel dimer configuration of a diatom Get3 forming a tetrameric complex with its tail-anchored membrane cargo | ||||||
![]() | ATPase ASNA1 homolog | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chang, H.Y. / Ko, T.P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A novel dimer configuration of a diatom Get3 forming a tetrameric complex with its tail-anchored membrane cargo Authors: Chang, H.Y. / Ko, T.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 307.9 KB | Display | ![]() |
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PDB format | ![]() | 209.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8hacC ![]() 2wojS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP
NCS oper: (Code: givenMatrix: (-0.046842484256, 0.998516634614, 0.0277544963513), (0.998596916564, 0.0474970664476, -0.0234142458491), (-0.0246977711247, 0.0266187730347, -0.99934051305)Vector: -29. ...NCS oper: (Code: given Matrix: (-0.046842484256, 0.998516634614, 0.0277544963513), Vector ![]() |
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Components
#1: Protein | Mass: 38836.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Production host: ![]() ![]() ![]() References: UniProt: B7G933, ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.37 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.07M sodium acetate, pH4.6, 5.6% PEG 4000, 30% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.81→30 Å / Num. obs: 9530 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 24.26 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 3.81→3.95 Å / Rmerge(I) obs: 1.016 / Num. unique obs: 931 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2WOJ Resolution: 3.81→29.82 Å / SU ML: 0.7159 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 38.3108 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.81→29.82 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.936618950995 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1 - 327
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