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Yorodumi- PDB-6x44: High Resolution Crystal Structure Analysis of SERA5 proenzyme fro... -
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-Basic information
Entry | Database: PDB / ID: 6x44 | ||||||
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Title | High Resolution Crystal Structure Analysis of SERA5 proenzyme 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 / symbiont-containing vacuole / regulation of immune response / cysteine-type peptidase activity / serine-type peptidase activity / proteolysis involved in protein catabolic process / kinase binding / peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases ...exit from host cell / symbiont-containing vacuolar space / symbiont-containing vacuole / regulation of immune response / cysteine-type peptidase activity / serine-type peptidase activity / proteolysis involved in protein catabolic process / kinase binding / peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lysosome / cysteine-type endopeptidase activity / proteolysis / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19733954166 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 | 6x44.cif.gz | 361.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x44.ent.gz | 238.4 KB | Display | PDB format |
PDBx/mmJSON format | 6x44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x44_validation.pdf.gz | 446 KB | Display | wwPDB validaton report |
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Full document | 6x44_full_validation.pdf.gz | 449.9 KB | Display | |
Data in XML | 6x44_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 6x44_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/6x44 ftp://data.pdbj.org/pub/pdb/validation_reports/x4/6x44 | HTTPS FTP |
-Related structure data
Related structure data | 6x42C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 50848.332 Da / Num. of mol.: 2 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) / Strain (production host): SHuffle T7 pLysY / References: UniProt: I0IYW5, UniProt: Q9TY95*PLUS #2: Chemical | ChemComp-PEG / | #3: Water | ChemComp-HOH / | 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: 2.69 Å3/Da / Density % sol: 54.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: LiSO4, Tris-HCl, PEG-4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0393 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0393 Å / Relative weight: 1 |
Reflection | Resolution: 2.197→47.55 Å / Num. obs: 56459 / % possible obs: 99.07 % / Redundancy: 7.3 % / Biso Wilson estimate: 34.5665711195 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1162 / Rpim(I) all: 0.04576 / Rrim(I) all: 0.1252 / Net I/σ(I): 11.56 |
Reflection shell | Resolution: 2.197→2.276 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.9169 / Num. unique obs: 5430 / CC1/2: 0.737 / Rpim(I) all: 0.3555 / Rrim(I) all: 0.9851 / % possible all: 97.12 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2wbf Resolution: 2.19733954166→47.5499422318 Å / SU ML: 0.238223530532 / Cross valid method: FREE R-VALUE / σ(F): 1.34004080654 / Phase error: 21.762703983 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: 46.2048237869 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.19733954166→47.5499422318 Å
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Refine LS restraints |
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LS refinement shell |
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