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Yorodumi- PDB-8gph: Crystal structure of protease 3C (C160A mutant) from Seneca Valle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gph | ||||||
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Title | Crystal structure of protease 3C (C160A mutant) from Seneca Valley Virus | ||||||
Components | Peptidase C3 | ||||||
Keywords | VIRAL PROTEIN / Seneca Valley virus / 3C protease / phospholipid | ||||||
Function / homology | Function and homology information T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / viral RNA genome replication / cysteine-type endopeptidase activity ...T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding Similarity search - Function | ||||||
Biological species | Senecavirus A | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.608 Å | ||||||
Authors | Zhao, H.F. / Zhang, H. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of protease 3C (C160A mutant) from Seneca Valley Virus Authors: Zhao, H.F. / Zhang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gph.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gph.ent.gz | 40.5 KB | Display | PDB format |
PDBx/mmJSON format | 8gph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/8gph ftp://data.pdbj.org/pub/pdb/validation_reports/gp/8gph | HTTPS FTP |
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-Related structure data
Related structure data | 6l0tS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22961.193 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Senecavirus A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U9IRU2 |
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#2: Chemical | ChemComp-PEG / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 4% (w/v) PEG 8000, 0.1 M HEPES (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9788 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 1.608→30 Å / Num. obs: 32177 / % possible obs: 97 % / Redundancy: 12 % / Biso Wilson estimate: 22.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.043 / Rrim(I) all: 0.059 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.61→1.69 Å / Redundancy: 8 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4383 / CC1/2: 0.858 / Rpim(I) all: 0.445 / Rrim(I) all: 0.619 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6L0T Resolution: 1.608→27.979 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.87 / 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: 62.59 Å2 / Biso mean: 26.9011 Å2 / Biso min: 15.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.608→27.979 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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