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Yorodumi- PDB-2pnl: Crystal structure of VP4 protease from infectious pancreatic necr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pnl | ||||||
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Title | Crystal structure of VP4 protease from infectious pancreatic necrosis virus (IPNV) in space group P1 | ||||||
Components | Protease VP4 | ||||||
Keywords | HYDROLASE / acyl-enzyme / protease / Ser/Lys dyad / viral protease / substrate complex / product complex | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / viral capsid / host cell cytoplasm / structural molecule activity / proteolysis / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Infectious pancreatic necrosis virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Paetzel, M. / Lee, J. / Feldman, A.R. / Delmas, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal structure of the VP4 protease from infectious pancreatic necrosis virus reveals the acyl-enzyme complex for an intermolecular self-cleavage reaction. Authors: Lee, J. / Feldman, A.R. / Delmas, B. / Paetzel, M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: Purification, crystallization and preliminary X-ray analysis of truncated and mutant forms of VP4 protease from infectious pancreatic necrosis virus. Authors: Lee, J. / Feldman, A.R. / Chiu, E. / Chan, C. / Kim, Y.-N. / Delmas, B. / Paetzel, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pnl.cif.gz | 402.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pnl.ent.gz | 338.8 KB | Display | PDB format |
PDBx/mmJSON format | 2pnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pnl_validation.pdf.gz | 512.7 KB | Display | wwPDB validaton report |
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Full document | 2pnl_full_validation.pdf.gz | 550.6 KB | Display | |
Data in XML | 2pnl_validation.xml.gz | 85.4 KB | Display | |
Data in CIF | 2pnl_validation.cif.gz | 120.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/2pnl ftp://data.pdbj.org/pub/pdb/validation_reports/pn/2pnl | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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10 |
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Unit cell |
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Details | the enzyme is a monomer in solution during purification, but forms an intermolecular acyl-enzyme complex with this construct, such that 6 of the 10 molecules in the asymmetric unit are linked via the nucleophile Ser633 and the C-terminal Ala716 (P1 residue of the VP4 internal cleavge site). |
-Components
#1: Protein | Mass: 21756.182 Da / Num. of mol.: 10 / Fragment: VP4tri (residues 514-716) / Mutation: K674A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Infectious pancreatic necrosis virus / Genus: Aquabirnavirus / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q703G9, UniProt: A1XQQ8*PLUS #2: Chemical | ChemComp-GAI / #3: 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: 2.5 Å3/Da / Density % sol: 50.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-HCl pH 8.5, 35% PEG 4000, 0.4M LiSO4, 0.4M Guanidine-HCl , VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2006 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→182.57 Å / Num. all: 103935 / Num. obs: 103935 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.21→2.29 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.5 / Num. unique all: 9718 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→182.57 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.883 / SU B: 6.397 / SU ML: 0.167 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.932 Å2
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Refinement step | Cycle: LAST / Resolution: 2.21→182.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.21→2.267 Å / Total num. of bins used: 20
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