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- PDB-3vx7: Crystal structure of Kluyveromyces marxianus Atg7NTD-Atg10 complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vx7 | ||||||
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Title | Crystal structure of Kluyveromyces marxianus Atg7NTD-Atg10 complex | ||||||
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![]() | LIGASE / ubiquitin conjugation / E1-E2 complex | ||||||
Function / homology | ![]() ubiquitin-like protein transferase activity / phagophore assembly site membrane / Transferases; Acyltransferases; Aminoacyltransferases / autophagy / protein transport Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamaguchi, M. / Matoba, K. / Sawada, R. / Fujioka, Y. / Nakatogawa, H. / Yamamoto, H. / Kobashigawa, Y. / Hoshida, H. / Akada, R. / Ohsumi, Y. ...Yamaguchi, M. / Matoba, K. / Sawada, R. / Fujioka, Y. / Nakatogawa, H. / Yamamoto, H. / Kobashigawa, Y. / Hoshida, H. / Akada, R. / Ohsumi, Y. / Noda, N.N. / Inagaki, F. | ||||||
![]() | ![]() Title: Noncanonical recognition and UBL loading of distinct E2s by autophagy-essential Atg7. Authors: Yamaguchi, M. / Matoba, K. / Sawada, R. / Fujioka, Y. / Nakatogawa, H. / Yamamoto, H. / Kobashigawa, Y. / Hoshida, H. / Akada, R. / Ohsumi, Y. / Noda, N.N. / 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 | ![]() | 96.1 KB | Display | ![]() |
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PDB format | ![]() | 72.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.5 KB | Display | ![]() |
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Full document | ![]() | 455.7 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vx6SC ![]() 3vx8C S: Starting model for refinement C: citing same article ( |
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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: 32213.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 17738.104 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
Sequence details | SEQUENCE DATABASE REFERENCE FOR EACH CHAIN DOES NOT CURRENTLY EXIST. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.36 Å3/Da / Density % sol: 77.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 0.8M sodium phosphate, 0.7M potassium phosphate, 0.2M lithium sulfate, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 8, 2010 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→49.69 Å / Num. all: 18726 / Num. obs: 18382 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Rsym value: 0.068 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 9.1 / Rsym value: 0.386 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3VX6 Resolution: 3.2→49.69 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 215793.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.718 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→49.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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