+Open data
-Basic information
Entry | Database: PDB / ID: 3ch3 | ||||||
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Title | Crystal Structure Analysis of SERA5E from plasmodium falciparum | ||||||
Components | Serine-repeat antigen protein | ||||||
Keywords | HYDROLASE / cysteine protease / papain family / Glycoprotein / Malaria / Thiol protease / Vacuole | ||||||
Function / homology | Function and homology information exit from host cell / symbiont-containing vacuolar space / MHC class II antigen presentation / symbiont-containing vacuole / Neutrophil degranulation / regulation of immune response / cysteine-type peptidase activity / serine-type peptidase activity / kinase binding / peptidase activity ...exit from host cell / symbiont-containing vacuolar space / MHC class II antigen presentation / symbiont-containing vacuole / Neutrophil degranulation / regulation of immune response / cysteine-type peptidase activity / serine-type peptidase activity / kinase binding / peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 Å | ||||||
Authors | Smith, B.J. / Malby, R.L. / Colman, P.M. / Clarke, O.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structural Insights into the Protease-like Antigen Plasmodium falciparum SERA5 and Its Noncanonical Active-Site Serine Authors: Hodder, A.N. / Malby, R.L. / Clarke, O.B. / Fairlie, W.D. / Colman, P.M. / Crabb, B.S. / Smith, B.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ch3.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ch3.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ch3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/3ch3 ftp://data.pdbj.org/pub/pdb/validation_reports/ch/3ch3 | HTTPS FTP |
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-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: 30664.244 Da / Num. of mol.: 1 Fragment: putative serine protease domain, UNP residues 564-828 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: SERA5 / Plasmid: pProExHTb / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9TY95 | ||
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#2: Chemical | ChemComp-K / | ||
#3: Chemical | #4: 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: 2.43 Å3/Da / Density % sol: 49.38 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2M KH2PO4, 12% PEG 8000, 5% PEG 400, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.968 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD |
Radiation | Monochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→24.74 Å / Num. obs: 26819 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.79→24.74 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.391 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.108 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.762 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→24.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→1.836 Å / Total num. of bins used: 20
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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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