+Open data
-Basic information
Entry | Database: PDB / ID: 6lj9 | ||||||||||||
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Title | Crystal Structure of Se-Met ASFV pS273R protease | ||||||||||||
Components | Cysteine protease S273R | ||||||||||||
Keywords | HYDROLASE | ||||||||||||
Function / homology | Function and homology information virion component / host cell cytoplasm / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / viral protein processing / cysteine-type endopeptidase activity / proteolysis Similarity search - Function | ||||||||||||
Biological species | African swine fever virus pig/Kenya/KEN-50/1950 | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.307 Å | ||||||||||||
Authors | Li, G.B. / Liu, X.X. / Chen, C. / Guo, Y. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: J.Virol. / Year: 2020 Title: Crystal Structure of African Swine Fever Virus pS273R Protease and Implications for Inhibitor Design. Authors: Li, G. / Liu, X. / Yang, M. / Zhang, G. / Wang, Z. / Guo, K. / Gao, Y. / Jiao, P. / Sun, J. / Chen, C. / Wang, H. / Deng, W. / Xiao, H. / Li, S. / Wu, H. / Wang, Y. / Cao, L. / Jia, Z. / ...Authors: Li, G. / Liu, X. / Yang, M. / Zhang, G. / Wang, Z. / Guo, K. / Gao, Y. / Jiao, P. / Sun, J. / Chen, C. / Wang, H. / Deng, W. / Xiao, H. / Li, S. / Wu, H. / Wang, Y. / Cao, L. / Jia, Z. / Shang, L. / Yang, C. / Guo, Y. / Rao, Z. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lj9.cif.gz | 224.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lj9.ent.gz | 187.5 KB | Display | PDB format |
PDBx/mmJSON format | 6lj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lj9_validation.pdf.gz | 434.3 KB | Display | wwPDB validaton report |
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Full document | 6lj9_full_validation.pdf.gz | 440.2 KB | Display | |
Data in XML | 6lj9_validation.xml.gz | 21 KB | Display | |
Data in CIF | 6lj9_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/6lj9 ftp://data.pdbj.org/pub/pdb/validation_reports/lj/6lj9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32915.051 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) African swine fever virus pig/Kenya/KEN-50/1950 Strain: isolate Pig/Kenya/KEN-50/1950 / Gene: Ken-123 / Production host: Escherichia coli (E. coli) References: UniProt: P0C9B9, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Water | ChemComp-HOH / | Has ligand of interest | N | Sequence details | Authors states that they modeled the MSE residues (114A, 115A) in the place with a good quality ...Authors states that they modeled the MSE residues (114A, 115A) in the place with a good quality electron density. Thus, there have both the Met and Mse residues in the coordinates. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.14 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Tris, pH 8.2, 23% w/v Polyethylene glycol 1,500 PH range: 8.0-8.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97911 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 2.079→48.843 Å / Num. obs: 21872 / % possible obs: 100 % / Redundancy: 7.04 % / CC1/2: 0.999 / Net I/σ(I): 10.67 |
Reflection shell | Resolution: 2.079→2.2 Å / Num. unique obs: 19824 / CC1/2: 0.715 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.307→48.769 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 198.15 Å2 / Biso mean: 47.3544 Å2 / Biso min: 9.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.307→48.769 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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