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Open data
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Basic information
Entry | Database: PDB / ID: 2dyt | ||||||
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Title | The crystal structure of Saccharomyces cerevisiae Atg3 | ||||||
![]() | Autophagy-related protein 3 | ||||||
![]() | LIGASE / E2 fold | ||||||
Function / homology | ![]() Atg8-family ligase activity / C-terminal protein lipidation / phagophore / glycophagy / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / phagophore assembly site ...Atg8-family ligase activity / C-terminal protein lipidation / phagophore / glycophagy / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / phagophore assembly site / protein targeting to membrane / autophagosome assembly / mitochondrion / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamada, Y. / Suzuki, N.N. / Inagaki, F. | ||||||
![]() | ![]() Title: The crystal structure of Atg3, an autophagy-related ubiquitin carrier protein (E2) enzyme that mediates Atg8 lipidation Authors: Yamada, Y. / Suzuki, N.N. / Hanada, T. / Ichimura, Y. / Kumeta, H. / Fujioka, Y. / Ohsumi, Y. / Inagaki, F. #1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2006 Title: Crystallization and preliminary X-ray analysis of Atg3 Authors: Yamada, Y. / Suzuki, N.N. / Fujioka, Y. / Ichimura, Y. / Ohsumi, Y. / Inagaki, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.2 KB | Display | ![]() |
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PDB format | ![]() | 40.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.7 KB | Display | ![]() |
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Full document | ![]() | 444.6 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 13.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36071.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 0.3M ammonium sulfate, 1.0M lithium sulfate, 0.1M citrate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 83016 / Num. obs: 83016 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 51.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 2.5→2.6 Å / Rmerge(I) obs: 0.271 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.775 Å2 / ksol: 0.37149 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→33.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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