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Yorodumi- PDB-1zyo: Crystal Structure of the Serine Protease Domain of Sesbania Mosai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zyo | ||||||
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Title | Crystal Structure of the Serine Protease Domain of Sesbania Mosaic Virus polyprotein | ||||||
Components | serine protease | ||||||
Keywords | HYDROLASE / viral serine protease of trypsin fold / beta-barrel / glutamyl endopeptidase | ||||||
Function / homology | Function and homology information host cell membrane / viral process / serine-type endopeptidase activity / proteolysis / membrane Similarity search - Function | ||||||
Biological species | Sesbania mosaic virus | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2.4 Å | ||||||
Authors | Gayathri, P. / Satheshkumar, P.S. / Prasad, K. / Savithri, H.S. / Murthy, M.R.N. | ||||||
Citation | Journal: Virology / Year: 2006 Title: Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket Authors: Gayathri, P. / Satheshkumar, P.S. / Prasad, K. / Nair, S. / Savithri, H.S. / Murthy, M.R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zyo.cif.gz | 44.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zyo.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 1zyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zyo_validation.pdf.gz | 434.8 KB | Display | wwPDB validaton report |
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Full document | 1zyo_full_validation.pdf.gz | 436.4 KB | Display | |
Data in XML | 1zyo_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 1zyo_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/1zyo ftp://data.pdbj.org/pub/pdb/validation_reports/zy/1zyo | HTTPS FTP |
-Related structure data
Related structure data | |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20430.281 Da / Num. of mol.: 1 / Fragment: protease domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sesbania mosaic virus / Genus: Sobemovirus / Gene: ORF2 / Plasmid: pRSET-C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9EB08, glutamyl endopeptidase |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-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: 52 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 8 Details: 0.2M Tris pH 8.0, 0.2M ammonium sulphate, 0.6M 1,6-hexane diol, 5mM mercaptoethanol, 4% glycerol, microbatch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 2, 2004 / Details: Osmic mirror |
Radiation | Monochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 9999 / Num. obs: 9272 / % possible obs: 92.73 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.12 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 32.13 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.09 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 3.8 / Num. unique all: 554 / % possible all: 56.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.879 / SU ML: 0.251 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.503 / ESU R Free: 0.306 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.831 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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