+Open data
-Basic information
Entry | Database: PDB / ID: 3ch2 | ||||||
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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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 | 3ch2.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ch2.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ch2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/3ch2 ftp://data.pdbj.org/pub/pdb/validation_reports/ch/3ch2 | HTTPS FTP |
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-Related structure data
Related structure data | 2wbfC 3ch3SC 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: 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-CA / |
#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: 2.43 Å3/Da / Density % sol: 49.34 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 18% PEG 3350, 0.2M CaCl2, unbuffered, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: capillary | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. obs: 26794 / % possible obs: 100 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3CH3 Resolution: 1.8→33.46 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.227 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.109 / 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: 26.619 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→33.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.799→1.846 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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