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Open data
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Basic information
Entry | Database: PDB / ID: 4j2g | ||||||
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Title | Atg13 HORMA domain | ||||||
![]() | KLTH0A00704p | ||||||
![]() | UNKNOWN FUNCTION / Autophagy / HORMA / Atg13 | ||||||
Function / homology | ![]() Atg1/ULK1 kinase complex / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phagophore assembly site / mitophagy / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jao, C. / Stanley, R.E. / Ragusa, M.J. / Hurley, J.H. | ||||||
![]() | ![]() Title: A HORMA domain in Atg13 mediates PI 3-kinase recruitment in autophagy. Authors: Jao, C.C. / Ragusa, M.J. / Stanley, R.E. / Hurley, J.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.9 KB | Display | ![]() |
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PDB format | ![]() | 73.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.1 KB | Display | ![]() |
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Full document | ![]() | 463.6 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 24.3 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: 30507.037 Da / Num. of mol.: 2 / Fragment: UNP residues 1-260 / Mutation: L123M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.16 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2mM ammonium sulfate, 0.1M MES pH6.5, 20% w/v PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 28, 2012 |
Radiation | Monochromator: filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→84.05 Å / Num. all: 29497 / % possible obs: 99 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 12.1 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.413 Å2
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Refinement step | Cycle: LAST / Resolution: 2.29→57.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.29→2.349 Å / Total num. of bins used: 20
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