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Yorodumi- PDB-6x42: High Resolution Crystal Structure Analysis of SERA5E from plasmod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x42 | ||||||
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Title | High Resolution Crystal Structure Analysis of SERA5E from plasmodium falciparum | ||||||
Components | Serine repeat antigen 5 | ||||||
Keywords | HYDROLASE / malaria / prodomain / protease | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Clarke, O.B. / Smith, N.A. / Lee, M. / Smith, B.J. | ||||||
Citation | Journal: Protein Sci. / Year: 2020 Title: Structure of the Plasmodium falciparum PfSERA5 pseudo-zymogen. Authors: Smith, N.A. / Clarke, O.B. / Lee, M. / Hodder, A.N. / 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 | 6x42.cif.gz | 195.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x42.ent.gz | 140.2 KB | Display | PDB format |
PDBx/mmJSON format | 6x42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/6x42 ftp://data.pdbj.org/pub/pdb/validation_reports/x4/6x42 | HTTPS FTP |
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-Related structure data
Related structure data | 6x44C 2wbfS 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
-Protein , 1 types, 1 molecules X
#1: Protein | Mass: 32928.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: sera5 / Production host: Escherichia coli (E. coli) / References: UniProt: I0IYY3, UniProt: Q9TY95*PLUS |
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-Non-polymers , 5 types, 244 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-I3C / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.19 Å3/Da / Density % sol: 43.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Bis-Tris, NaCl, KH2PO4, PEG-8000, PEG-400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.956619 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.956619 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→24.47 Å / Num. obs: 87458 / % possible obs: 99.92 % / Redundancy: 11.2 % / Biso Wilson estimate: 15.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06326 / Rpim(I) all: 0.01989 / Rrim(I) all: 0.06635 / Net I/σ(I): 17.72 |
Reflection shell | Resolution: 1.2→1.243 Å / Redundancy: 10.6 % / Num. unique obs: 8714 / CC1/2: 0.453 / % possible all: 99.46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WBF Resolution: 1.2→24.47 Å / SU ML: 0.1184 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 15.4447 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 24.39 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→24.47 Å
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Refine LS restraints |
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LS refinement shell |
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