+Open data
-Basic information
Entry | Database: PDB / ID: 4xfq | ||||||
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Title | Crystal Structure Basis for PEDV 3C Like Protease | ||||||
Components | PEDV main protease | ||||||
Keywords | HYDROLASE / Porcine epidemic diarrhea virus / 3C-Like Protease | ||||||
Function / homology | Function and homology information host cell membrane / viral genome replication / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity ...host cell membrane / viral genome replication / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Porcine epidemic diarrhea virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Ye, G. / Fu, Z.F. / Peng, G.Q. | ||||||
Citation | Journal: Virology / Year: 2016 Title: Structural basis for the dimerization and substrate recognition specificity of porcine epidemic diarrhea virus 3C-like protease. Authors: Ye, G. / Deng, F. / Shen, Z. / Luo, R. / Zhao, L. / Xiao, S. / Fu, Z.F. / Peng, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xfq.cif.gz | 133 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xfq.ent.gz | 102.7 KB | Display | PDB format |
PDBx/mmJSON format | 4xfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xfq_validation.pdf.gz | 435.7 KB | Display | wwPDB validaton report |
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Full document | 4xfq_full_validation.pdf.gz | 440.8 KB | Display | |
Data in XML | 4xfq_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 4xfq_validation.cif.gz | 39.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/4xfq ftp://data.pdbj.org/pub/pdb/validation_reports/xf/4xfq | HTTPS FTP |
-Related structure data
Related structure data | 4zuhC 1p9sS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 33295.641 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2998-3295 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porcine epidemic diarrhea virus / Gene: Pol1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: K4L9I6 #2: Water | ChemComp-HOH / | |
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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: 2.27 Å3/Da / Density % sol: 45.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 5% PEG3350, 0.1M NaCl, 0.2M Na2HPO4:Citric Acid pH 4.2 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97917 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97917 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→50 Å / Num. obs: 69155 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.75 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.033 / Rrim(I) all: 0.064 / Χ2: 1.234 / Net I/av σ(I): 23.249 / Net I/σ(I): 13 / Num. measured all: 257484 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P9S Resolution: 1.65→27.454 Å / FOM work R set: 0.849 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.2 / 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: 66.42 Å2 / Biso mean: 24.85 Å2 / Biso min: 10.22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→27.454 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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