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Open data
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Basic information
Entry | Database: PDB / ID: 7wlh | ||||||
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Title | The crystal structure of African swine fever virus I215L | ||||||
![]() | E2 ubiquitin-conjugating enzyme | ||||||
![]() | TRANSFERASE / ASFV / I215L / VIRAL PROTEIN | ||||||
Function / homology | ![]() E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / host cell cytoplasm / protein ubiquitination / host cell nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shen, Z. / Liang, R. / Yang, Y. / Peng, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The crystal structure of African swine fever virus I215L Authors: Shen, Z. / Liang, R. / Yang, Y. / Peng, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.8 KB | Display | ![]() |
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PDB format | ![]() | 32.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 22932.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: I215L CDS, I215L, ASFV-Georgia_4-165, ASFV_Kyiv_2016_131_00221 Production host: ![]() ![]() References: UniProt: A0A2X0TKQ7, E2 ubiquitin-conjugating enzyme |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.06 Å3/Da / Density % sol: 75.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium Acetate: HCl (pH 4.6), and 2.8 M Sodium Formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.65→50 Å / Num. obs: 12713 / % possible obs: 94.5 % / Redundancy: 17.8 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.023 / Rrim(I) all: 0.101 / Χ2: 0.62 / Net I/σ(I): 5.6 / Num. measured all: 226540 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 207.37 Å2 / Biso mean: 60 Å2 / Biso min: 60.43 Å2
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Refinement step | Cycle: final / Resolution: 2.65→35.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.652→2.721 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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