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Yorodumi- PDB-3s5h: Crystal structures of falcilysin, a M16 metalloprotease from the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s5h | ||||||
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Title | Crystal structures of falcilysin, a M16 metalloprotease from the malaria parasite Plasmodium falciparum | ||||||
Components | Falcilysin | ||||||
Keywords | HYDROLASE / M16 metalloprotease / peptidase | ||||||
Function / homology | Function and homology information hemoglobin catabolic process / apicoplast / food vacuole / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / vacuolar membrane / chloroplast / protein processing / metalloendopeptidase activity / mitochondrial matrix / metal ion binding Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.603 Å | ||||||
Authors | Morgunova, E. / Ponpuak, M. / Istvan, E. / Popov, A. / Goldberg, D. / Eneqvist, T. | ||||||
Citation | Journal: To be Published Title: Crystal structures of falcilysin, a M16 metalloprotease from the malaria parasite Plasmodium falciparum Authors: Morgunova, E. / Ponpuak, M. / Istvan, E. / Popov, A. / Goldberg, D. / Eneqvist, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s5h.cif.gz | 441 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s5h.ent.gz | 360.6 KB | Display | PDB format |
PDBx/mmJSON format | 3s5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s5h_validation.pdf.gz | 428.9 KB | Display | wwPDB validaton report |
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Full document | 3s5h_full_validation.pdf.gz | 445.8 KB | Display | |
Data in XML | 3s5h_validation.xml.gz | 46.2 KB | Display | |
Data in CIF | 3s5h_validation.cif.gz | 68.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/3s5h ftp://data.pdbj.org/pub/pdb/validation_reports/s5/3s5h | HTTPS FTP |
-Related structure data
Related structure data | 3s5iC 3s5kC 3s5mC 2fgeS C: citing same article (ref.) S: Starting model for refinement |
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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: 139050.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: HB3 / Gene: flN, PF13_0322 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q76NL8 |
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#2: Chemical | ChemComp-CO / |
#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: 2.35 Å3/Da / Density % sol: 47.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 11% PEG6000,10%PEG400,0.1M ADA, 20mM Mg acetate,20 mM Co acetate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2010 / Details: bent cylindrical mirror |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→49.6 Å / Num. obs: 310281 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.26 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.3 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FGE Resolution: 1.603→49.474 Å / SU ML: 0.26 / Isotropic thermal model: isotropic / σ(F): 0.12 / Phase error: 23.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.15 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.603→49.474 Å
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Refine LS restraints |
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LS refinement shell |
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